From cfba642d8b94f39ee6d9187d767408b17937cda8 Mon Sep 17 00:00:00 2001
From: vqdang <24943262+vqdang@users.noreply.github.com>
Date: Mon, 29 Jan 2024 15:33:57 +0000
Subject: [PATCH 01/36] UPD: fix bound

---
 tiatoolbox/wsicore/wsireader.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tiatoolbox/wsicore/wsireader.py b/tiatoolbox/wsicore/wsireader.py
index 49e9180fa..ee0dfecaa 100644
--- a/tiatoolbox/wsicore/wsireader.py
+++ b/tiatoolbox/wsicore/wsireader.py
@@ -4071,7 +4071,7 @@ class docstrings for more information.
             # but base image is of different scale)
             (
                 read_level,
-                _,
+                bounds_at_read_level,
                 _,
                 post_read_scale,
             ) = self._find_read_bounds_params(
@@ -4083,7 +4083,7 @@ class docstrings for more information.
             # Find parameters for optimal read
             (
                 read_level,
-                _,
+                bounds_at_read_level,
                 size_at_requested,
                 post_read_scale,
             ) = self._find_read_bounds_params(
@@ -4094,7 +4094,7 @@ class docstrings for more information.
 
         im_region = utils.image.sub_pixel_read(
             image=self.level_arrays[read_level],
-            bounds=bounds_at_baseline,
+            bounds=bounds_at_read_level,
             output_size=size_at_requested,
             interpolation=interpolation,
             pad_mode=pad_mode,

From 6fdf9e704f3fcd4ab685e239b0b0d269539df40b Mon Sep 17 00:00:00 2001
From: Abdol A <u2271662@live.warwick.ac.uk>
Date: Mon, 13 May 2024 15:04:45 +0100
Subject: [PATCH 02/36] =?UTF-8?q?=E2=9C=85=20Add=20test?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 tests/test_wsireader.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/tests/test_wsireader.py b/tests/test_wsireader.py
index e8d0f28da..921b26d04 100644
--- a/tests/test_wsireader.py
+++ b/tests/test_wsireader.py
@@ -974,6 +974,27 @@ def test_read_bounds_level_consistency_jp2(sample_jp2: Path) -> None:
     read_bounds_level_consistency(wsi, bounds)
 
 
+def test_read_bounds_tiff_wsi_reader(sample_svs: Path) -> None:
+    """Test read_bounds with TIFFWSIReader."""
+    reader = TIFFWSIReader(sample_svs)
+    slide_dimensions = reader.info.slide_dimensions
+    bounds = (0, 0, *slide_dimensions)
+    resolution = reader.info.mpp
+    coord_spaces = ["baseline", "resolution"]
+    for coord_space in coord_spaces:
+        im_region = reader.read_bounds(
+            bounds=bounds,
+            resolution=resolution,
+            units="mpp",
+            interpolation="nearest",
+            coord_space=coord_space,
+        )
+        expected_output_shape = tuple(np.round(slide_dimensions[::-1]).astype(int))
+        assert isinstance(im_region, np.ndarray)
+        assert im_region.shape[2] == 3
+        assert im_region.shape[:2] == pytest.approx(expected_output_shape, abs=1)
+
+
 def test_wsireader_save_tiles(sample_svs: Path, tmp_path: Path) -> None:
     """Test for save_tiles in wsireader as a python function."""
     tmp_path = Path(tmp_path)

From 609469d87b02865ec27b309646057e7451cf801b Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Fri, 21 Jun 2024 18:31:02 +0100
Subject: [PATCH 03/36] initial draft multichannel reading

---
 tiatoolbox/utils/postproc_defs.py          |  68 +++++++++
 tiatoolbox/visualization/bokeh_app/main.py |  21 ++-
 tiatoolbox/wsicore/wsireader.py            | 158 +++++++++++++++++----
 3 files changed, 217 insertions(+), 30 deletions(-)
 create mode 100644 tiatoolbox/utils/postproc_defs.py

diff --git a/tiatoolbox/utils/postproc_defs.py b/tiatoolbox/utils/postproc_defs.py
new file mode 100644
index 000000000..91e5fc6ec
--- /dev/null
+++ b/tiatoolbox/utils/postproc_defs.py
@@ -0,0 +1,68 @@
+"""Module to provide postprocessing classes."""
+
+from __future__ import annotations
+
+import colorsys
+
+import numpy as np
+
+
+class MultichannelToRGB:
+    """Class to convert multi-channel images to RGB images."""
+
+    def __init__(
+        self: MultichannelToRGB,
+        default_colors: list[tuple[float, float, float]] | None = None,
+    ) -> None:
+        """Initialize the MultichannelToRGB converter.
+
+        Args:
+            default_colors: List of default RGB colors for each channel. If not
+            provided, colors will be auto-generated using the HSV color space.
+
+        """
+        self.default_colors = default_colors
+        if self.default_colors is not None:
+            self.default_colors = np.array(self.default_colors, dtype=np.float32)
+
+    def generate_colors(self: MultichannelToRGB, n_channels: int) -> np.ndarray:
+        """Generate a set of visually distinct colors.
+
+        Args:
+            n_channels (int): Number of channels/colors to generate
+
+        Returns:
+            np.ndarray: Array of RGB colors
+
+        """
+        return np.array(
+            [colorsys.hsv_to_rgb(i / n_channels, 1, 1) for i in range(n_channels)],
+            dtype=np.float32,
+        )
+
+    def __call__(self: MultichannelToRGB, image: np.ndarray) -> np.ndarray:
+        """Convert a multi-channel image to an RGB image.
+
+        Args:
+            image (np.ndarray): Input image of shape (H, W, N)
+
+        Returns:
+            np.ndarray: RGB image of shape (H, W, 3)
+
+        """
+        n = image.shape[2]
+
+        if n < 5:  # noqa: PLR2004
+            # assume already rgb(a) so just return image
+            return image
+
+        if self.default_colors is None:
+            colors = self.generate_colors(n)
+        else:
+            colors = self.default_colors
+
+        # Convert to RGB image
+        rgb_image = np.einsum("hwn,nc->hwc", image, colors, optimize=True)
+
+        # Clip  to ensure in valid range and return
+        return np.clip(rgb_image, 0, 255).astype(np.uint8)
diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index bdd612e3a..b58ae529e 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -725,7 +725,16 @@ def populate_slide_list(slide_folder: Path, search_txt: str | None = None) -> No
     """Populate the slide list with the available slides."""
     file_list = []
     len_slidepath = len(slide_folder.parts)
-    for ext in ["*.svs", "*ndpi", "*.tiff", "*.mrxs", "*.jpg", "*.png", "*.tif"]:
+    for ext in [
+        "*.svs",
+        "*.ndpi",
+        "*.tiff",
+        "*.mrxs",
+        "*.jpg",
+        "*.png",
+        "*.tif",
+        "*.qptiff",
+    ]:
         file_list.extend(list(Path(slide_folder).glob(str(Path("*") / ext))))
         file_list.extend(list(Path(slide_folder).glob(ext)))
     if search_txt is None:
@@ -2086,7 +2095,15 @@ def setup_doc(self: DocConfig, base_doc: Document) -> tuple[Row, Tabs]:
 
         # Set initial slide to first one in base folder
         slide_list = []
-        for ext in ["*.svs", "*ndpi", "*.tiff", "*.mrxs", "*.png", "*.jpg"]:
+        for ext in [
+            "*.svs",
+            "*.ndpi",
+            "*.tiff",
+            "*.mrxs",
+            "*.png",
+            "*.jpg",
+            "*.qptiff",
+        ]:
             slide_list.extend(list(doc_config["slide_folder"].glob(ext)))
             slide_list.extend(
                 list(doc_config["slide_folder"].glob(str(Path("*") / ext))),
diff --git a/tiatoolbox/wsicore/wsireader.py b/tiatoolbox/wsicore/wsireader.py
index 00e8b7673..f6532cd7d 100644
--- a/tiatoolbox/wsicore/wsireader.py
+++ b/tiatoolbox/wsicore/wsireader.py
@@ -24,6 +24,7 @@
 
 from tiatoolbox import logger, utils
 from tiatoolbox.annotation import AnnotationStore, SQLiteStore
+from tiatoolbox.utils import postproc_defs
 from tiatoolbox.utils.env_detection import pixman_warning
 from tiatoolbox.utils.exceptions import FileNotSupportedError
 from tiatoolbox.utils.magic import is_sqlite3
@@ -258,7 +259,10 @@ def np_virtual_wsi(
 
 
 def _handle_tiff_wsi(
-    input_path: Path, mpp: tuple[Number, Number] | None, power: Number | None
+    input_path: Path,
+    mpp: tuple[Number, Number] | None,
+    power: Number | None,
+    post_proc: str | callable | None,
 ) -> TIFFWSIReader | OpenSlideWSIReader | None:
     """Handle TIFF WSI cases.
 
@@ -271,6 +275,8 @@ def _handle_tiff_wsi(
         power (:obj:`float` or :obj:`None`, optional):
             The objective power of the WSI. If not provided, the power
             is approximated from the MPP.
+        post_proc (str | callable | None):
+            Post-processing function to apply to the image.
 
     Returns:
         OpenSlideWSIReader | TIFFWSIReader | None:
@@ -280,11 +286,13 @@ def _handle_tiff_wsi(
     """
     if openslide.OpenSlide.detect_format(input_path) is not None:
         try:
-            return OpenSlideWSIReader(input_path, mpp=mpp, power=power)
+            return OpenSlideWSIReader(
+                input_path, mpp=mpp, power=power, post_proc=post_proc
+            )
         except openslide.OpenSlideError:
             pass
     if is_tiled_tiff(input_path):
-        return TIFFWSIReader(input_path, mpp=mpp, power=power)
+        return TIFFWSIReader(input_path, mpp=mpp, power=power, post_proc=post_proc)
 
     return None
 
@@ -308,6 +316,10 @@ class WSIReader:
         power (:obj:`float` or :obj:`None`, optional):
             The objective power of the WSI. If not provided, the power
             is approximated from the MPP.
+        post_proc (str | callable | None):
+            Post-processing function to apply to the image. If None,
+            no post-processing is applied. If 'auto', the post-processing
+            function is automatically selected based on the reader type.
 
     """
 
@@ -316,6 +328,7 @@ def open(  # noqa: PLR0911
         input_img: str | Path | np.ndarray | WSIReader,
         mpp: tuple[Number, Number] | None = None,
         power: Number | None = None,
+        post_proc: str | callable | None = "auto",
         **kwargs: dict,
     ) -> WSIReader:
         """Return an appropriate :class:`.WSIReader` object.
@@ -334,6 +347,10 @@ def open(  # noqa: PLR0911
                 (x, y) tuple of the MPP in the units of the input image.
             power (float):
                 Objective power of the input image.
+            post_proc (str | callable | None):
+                Post-processing function to apply to the image. If None,
+                no post-processing is applied. If 'auto', the post-processing
+                function is automatically selected based on the reader type.
             kwargs (dict):
                 Key-word arguments.
 
@@ -353,7 +370,9 @@ def open(  # noqa: PLR0911
                 msg,
             )
         if isinstance(input_img, np.ndarray):
-            return VirtualWSIReader(input_img, mpp=mpp, power=power)
+            return VirtualWSIReader(
+                input_img, mpp=mpp, power=power, post_proc=post_proc
+            )
 
         if isinstance(input_img, WSIReader):
             return input_img
@@ -364,12 +383,13 @@ def open(  # noqa: PLR0911
 
         # Handle special cases first (DICOM, Zarr/NGFF, OME-TIFF)
         if is_dicom(input_path):
-            return DICOMWSIReader(input_path, mpp=mpp, power=power)
+            return DICOMWSIReader(input_path, mpp=mpp, power=power, post_proc=post_proc)
 
         _, _, suffixes = utils.misc.split_path_name_ext(input_path)
         last_suffix = suffixes[-1]
 
         if last_suffix == ".db":
+            kwargs["post_proc"] = post_proc
             return AnnotationStoreReader(input_path, **kwargs)
 
         if last_suffix in (".zarr",):
@@ -381,10 +401,15 @@ def open(  # noqa: PLR0911
             return NGFFWSIReader(input_path, mpp=mpp, power=power)
 
         if suffixes[-2:] in ([".ome", ".tiff"],):
-            return TIFFWSIReader(input_path, mpp=mpp, power=power)
+            return TIFFWSIReader(input_path, mpp=mpp, power=power, post_proc=post_proc)
+
+        if last_suffix == ".qptiff":
+            return TIFFWSIReader(input_path, mpp=mpp, power=power, post_proc=post_proc)
 
         if last_suffix in (".tif", ".tiff"):
-            tiff_wsi = _handle_tiff_wsi(input_path, mpp=mpp, power=power)
+            tiff_wsi = _handle_tiff_wsi(
+                input_path, mpp=mpp, power=power, post_proc=post_proc
+            )
             if tiff_wsi is not None:
                 return tiff_wsi
 
@@ -396,7 +421,7 @@ def open(  # noqa: PLR0911
             return virtual_wsi
 
         # Try openslide last
-        return OpenSlideWSIReader(input_path, mpp=mpp, power=power)
+        return OpenSlideWSIReader(input_path, mpp=mpp, power=power, post_proc=post_proc)
 
     @staticmethod
     def verify_supported_wsi(input_path: Path) -> None:
@@ -429,6 +454,7 @@ def verify_supported_wsi(input_path: Path) -> None:
             ".jpeg",
             ".zarr",
             ".db",
+            ".qptiff",
         ]:
             msg = f"File {input_path} is not a supported file format."
             raise FileNotSupportedError(
@@ -440,6 +466,7 @@ def __init__(
         input_img: str | Path | np.ndarray | AnnotationStore,
         mpp: tuple[Number, Number] | None = None,
         power: Number | None = None,
+        post_proc: callable | None = None,
     ) -> None:
         """Initialize :class:`WSIReader`."""
         if isinstance(input_img, (np.ndarray, AnnotationStore)):
@@ -464,6 +491,7 @@ def __init__(
             msg = "`power` must be a number."
             raise TypeError(msg)
         self._manual_power = power
+        self.post_proc = self.get_post_proc(post_proc)
 
     @property
     def info(self: WSIReader) -> WSIMeta:
@@ -495,6 +523,35 @@ def info(self: WSIReader, meta: WSIMeta) -> None:
         """
         self._m_info = meta
 
+    def get_post_proc(self: WSIReader, post_proc: str | callable | None) -> callable:
+        """Get the post-processing function.
+
+        Args:
+            post_proc (str | callable | None):
+                Post-processing function to apply to the image. If auto,
+                will use no post_proc unless reader is TIFF or Virtual Reader,
+                in which case it will use MultichannelToRGB.
+
+        Returns:
+            callable:
+                Post-processing function.
+
+        """
+        if callable(post_proc):
+            return post_proc
+        if post_proc is None:
+            return None
+        if post_proc == "auto":
+            # if its TIFFWSIReader or VirtualWSIReader, return fn to
+            # allow multichannel, else return None
+            if isinstance(self, (TIFFWSIReader, VirtualWSIReader)):
+                return postproc_defs.MultichannelToRGB()
+            return None
+        if isinstance(post_proc, str) and hasattr(postproc_defs, post_proc):
+            return getattr(postproc_defs, post_proc)()
+        msg = f"Invalid post-processing function: {post_proc}"
+        raise ValueError(msg)
+
     def _info(self: WSIReader) -> WSIMeta:
         """WSI metadata internal getter used to update info property.
 
@@ -1724,9 +1781,10 @@ def __init__(
         input_img: str | Path | np.ndarray,
         mpp: tuple[Number, Number] | None = None,
         power: Number | None = None,
+        post_proc: str | callable | None = "auto",
     ) -> None:
         """Initialize :class:`OpenSlideWSIReader`."""
-        super().__init__(input_img=input_img, mpp=mpp, power=power)
+        super().__init__(input_img=input_img, mpp=mpp, power=power, post_proc=post_proc)
         self.openslide_wsi = openslide.OpenSlide(filename=str(self.input_path))
 
     def read_rect(
@@ -1969,6 +2027,8 @@ def read_rect(
             interpolation=interpolation,
         )
 
+        if self.post_proc is not None:
+            im_region = self.post_proc(im_region)
         return utils.transforms.background_composite(image=im_region, alpha=False)
 
     def read_bounds(
@@ -2154,6 +2214,8 @@ class docstrings for more information.
                 interpolation=interpolation,
             )
 
+        if self.post_proc is not None:
+            im_region = self.post_proc(im_region)
         return utils.transforms.background_composite(image=im_region, alpha=False)
 
     @staticmethod
@@ -2262,9 +2324,10 @@ def __init__(
         input_img: str | Path | np.ndarray,
         mpp: tuple[Number, Number] | None = None,
         power: Number | None = None,
+        post_proc: str | callable | None = "auto",
     ) -> None:
         """Initialize :class:`OmnyxJP2WSIReader`."""
-        super().__init__(input_img=input_img, mpp=mpp, power=power)
+        super().__init__(input_img=input_img, mpp=mpp, power=power, post_proc=post_proc)
         import glymur
 
         glymur.set_option("lib.num_threads", os.cpu_count() or 1)
@@ -2508,6 +2571,8 @@ def read_rect(
             interpolation=interpolation,
         )
 
+        if self.post_proc is not None:
+            im_region = self.post_proc(im_region)
         return utils.transforms.background_composite(image=im_region, alpha=False)
 
     def read_bounds(
@@ -2682,6 +2747,8 @@ class docstrings for more information.
                 interpolation=interpolation,
             )
 
+        if self.post_proc is not None:
+            im_region = self.post_proc(im_region)
         return utils.transforms.background_composite(image=im_region, alpha=False)
 
     @staticmethod
@@ -2879,6 +2946,8 @@ class VirtualWSIReader(WSIReader):
             "bool" mode supports binary masks,
             interpolation in this case will be "nearest" instead of "bicubic".
             "feature" mode allows multichannel features.
+        post_proc (str, callable):
+            Post-processing function to apply to the output image.
 
     """
 
@@ -2889,12 +2958,14 @@ def __init__(
         power: Number | None = None,
         info: WSIMeta | None = None,
         mode: str = "rgb",
+        post_proc: str | callable | None = "auto",
     ) -> None:
         """Initialize :class:`VirtualWSIReader`."""
         super().__init__(
             input_img=input_img,
             mpp=mpp,
             power=power,
+            post_proc=post_proc,
         )
         if mode.lower() not in ["rgb", "bool", "feature"]:
             msg = "Invalid mode."
@@ -3216,6 +3287,8 @@ def read_rect(
         )
 
         if self.mode == "rgb":
+            if self.post_proc is not None:
+                im_region = self.post_proc(im_region)
             return utils.transforms.background_composite(image=im_region, alpha=False)
         return im_region
 
@@ -3393,6 +3466,8 @@ class docstrings for more information.
             )
 
         if self.mode == "rgb":
+            if self.post_proc is not None:
+                im_region = self.post_proc(im_region)
             return utils.transforms.background_composite(image=im_region, alpha=False)
         return im_region
 
@@ -3456,12 +3531,13 @@ def __init__(
         mpp: tuple[Number, Number] | None = None,
         power: Number | None = None,
         series: str = "auto",
-        cache_size: int = 2**28,
+        cache_size: int = 2**28,  # noqa: ARG002
+        post_proc: str | callable | None = "auto",
     ) -> None:
         """Initialize :class:`TIFFWSIReader`."""
-        super().__init__(input_img=input_img, mpp=mpp, power=power)
+        super().__init__(input_img=input_img, mpp=mpp, power=power, post_proc=post_proc)
         self.tiff = tifffile.TiffFile(self.input_path)
-        self._axes = self.tiff.pages[0].axes
+        self._axes = self.tiff.series[0].axes
         # Flag which is True if the image is a simple single page tile TIFF
         is_single_page_tiled = all(
             [
@@ -3472,7 +3548,14 @@ def __init__(
                 len(self.tiff.pages) == 1,
             ],
         )
-        if not any([self.tiff.is_svs, self.tiff.is_ome, is_single_page_tiled]):
+        if not any(
+            [
+                self.tiff.is_svs,
+                self.tiff.is_ome,
+                is_single_page_tiled,
+                self.tiff.is_bigtiff,
+            ]
+        ):
             msg = "Unsupported TIFF WSI format."
             raise ValueError(msg)
 
@@ -3486,7 +3569,7 @@ def __init__(
 
             def page_area(page: tifffile.TiffPage) -> float:
                 """Calculate the area of a page."""
-                return np.prod(self._canonical_shape(page.shape)[:2])
+                return np.prod(self._canonical_shape(page.shape)[:2], dtype=float)
 
             series_areas = [page_area(s.pages[0]) for s in all_series]  # skipcq
             self.series_n = np.argmax(series_areas)
@@ -3496,8 +3579,8 @@ def page_area(page: tifffile.TiffPage) -> float:
             series=self.series_n,
             aszarr=True,
         )
-        self._zarr_lru_cache = zarr.LRUStoreCache(self._zarr_store, max_size=cache_size)
-        self._zarr_group = zarr.open(self._zarr_lru_cache)
+        # remove LRU cache for now as seems to cause issues on windows
+        self._zarr_group = zarr.open(self._zarr_store)
         if not isinstance(self._zarr_group, zarr.hierarchy.Group):
             group = zarr.hierarchy.group()
             group[0] = self._zarr_group
@@ -3516,12 +3599,12 @@ def _canonical_shape(self: TIFFWSIReader, shape: IntPair) -> tuple:
 
         Returns:
             tuple:
-                Shape in YXS order.
+                Shape in YXS or YXC order.
 
         """
-        if self._axes == "YXS":
+        if self._axes in ("YXS", "YXC"):
             return shape
-        if self._axes == "SYX":
+        if self._axes in ("SYX", "CYX"):
             return np.roll(shape, -1)
         msg = f"Unsupported axes `{self._axes}`."
         raise ValueError(msg)
@@ -4002,13 +4085,15 @@ def read_rect(
                 pad_mode=pad_mode,
                 pad_constant_values=pad_constant_values,
             )
+            if self.post_proc is not None:
+                im_region = self.post_proc(im_region)
             return utils.transforms.background_composite(im_region, alpha=False)
 
         # Find parameters for optimal read
         (
             read_level,
-            _,
-            _,
+            level_read_location,
+            level_read_size,
             post_read_scale,
             baseline_read_size,
         ) = self.find_read_rect_params(
@@ -4019,8 +4104,8 @@ def read_rect(
         )
 
         bounds = utils.transforms.locsize2bounds(
-            location=location,
-            size=baseline_read_size,
+            location=level_read_location,
+            size=level_read_size,
         )
         im_region = utils.image.safe_padded_read(
             image=self.level_arrays[read_level],
@@ -4036,6 +4121,8 @@ def read_rect(
             interpolation=interpolation,
         )
 
+        if self.post_proc is not None:
+            im_region = self.post_proc(im_region)
         return utils.transforms.background_composite(image=im_region, alpha=False)
 
     def read_bounds(
@@ -4163,7 +4250,7 @@ class docstrings for more information.
             # but base image is of different scale)
             (
                 read_level,
-                _,
+                bounds_at_read_level,
                 _,
                 post_read_scale,
             ) = self._find_read_bounds_params(
@@ -4175,7 +4262,7 @@ class docstrings for more information.
             # Find parameters for optimal read
             (
                 read_level,
-                _,
+                bounds_at_read_level,
                 size_at_requested,
                 post_read_scale,
             ) = self._find_read_bounds_params(
@@ -4186,7 +4273,7 @@ class docstrings for more information.
 
         im_region = utils.image.sub_pixel_read(
             image=self.level_arrays[read_level],
-            bounds=bounds_at_baseline,
+            bounds=bounds_at_read_level,
             output_size=size_at_requested,
             interpolation=interpolation,
             pad_mode=pad_mode,
@@ -4208,6 +4295,8 @@ class docstrings for more information.
                 output_size=size_at_requested,
             )
 
+        if self.post_proc is not None:
+            return self.post_proc(im_region)
         return im_region
 
 
@@ -4221,11 +4310,12 @@ def __init__(
         input_img: str | Path | np.ndarray,
         mpp: tuple[Number, Number] | None = None,
         power: Number | None = None,
+        post_proc: str | callable | None = "auto",
     ) -> None:
         """Initialize :class:`DICOMWSIReader`."""
         from wsidicom import WsiDicom
 
-        super().__init__(input_img, mpp, power)
+        super().__init__(input_img, mpp, power, post_proc)
         self.wsi = WsiDicom.open(input_img)
 
     def _info(self: DICOMWSIReader) -> WSIMeta:
@@ -4517,6 +4607,8 @@ def read_rect(
             interpolation=interpolation,
         )
 
+        if self.post_proc is not None:
+            im_region = self.post_proc(im_region)
         return utils.transforms.background_composite(image=im_region, alpha=False)
 
     def read_bounds(
@@ -4712,6 +4804,8 @@ class docstrings for more information.
                 interpolation=interpolation,
             )
 
+        if self.post_proc is not None:
+            return self.post_proc(im_region)
         return utils.transforms.background_composite(image=im_region, alpha=False)
 
 
@@ -5035,6 +5129,8 @@ def read_rect(
                 pad_mode=pad_mode,
                 pad_constant_values=pad_constant_values,
             )
+            if self.post_proc is not None:
+                return self.post_proc(im_region)
             return utils.transforms.background_composite(image=im_region, alpha=False)
 
         # Find parameters for optimal read
@@ -5069,6 +5165,8 @@ def read_rect(
             interpolation=interpolation,
         )
 
+        if self.post_proc is not None:
+            im_region = self.post_proc(im_region)
         return utils.transforms.background_composite(image=im_region, alpha=False)
 
     def read_bounds(
@@ -5606,6 +5704,8 @@ def read_rect(
                 coord_space=coord_space,
                 **kwargs,
             )
+            if self.post_proc is not None:
+                base_region = self.post_proc(base_region)
             base_region = Image.fromarray(
                 utils.transforms.background_composite(base_region, alpha=True),
             )
@@ -5799,6 +5899,8 @@ class docstrings for more information.
                 coord_space=coord_space,
                 **kwargs,
             )
+            if self.post_proc is not None:
+                base_region = self.post_proc(base_region)
             base_region = Image.fromarray(
                 utils.transforms.background_composite(base_region, alpha=True),
             )

From aec8390659279f0506b6b3c203d861efb768a360 Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Fri, 21 Jun 2024 19:05:59 +0100
Subject: [PATCH 04/36] deepsource

---
 tiatoolbox/utils/postproc_defs.py | 3 ++-
 tiatoolbox/wsicore/wsireader.py   | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/tiatoolbox/utils/postproc_defs.py b/tiatoolbox/utils/postproc_defs.py
index 91e5fc6ec..5b9ec505a 100644
--- a/tiatoolbox/utils/postproc_defs.py
+++ b/tiatoolbox/utils/postproc_defs.py
@@ -25,7 +25,8 @@ def __init__(
         if self.default_colors is not None:
             self.default_colors = np.array(self.default_colors, dtype=np.float32)
 
-    def generate_colors(self: MultichannelToRGB, n_channels: int) -> np.ndarray:
+    @staticmethod
+    def generate_colors(n_channels: int) -> np.ndarray:
         """Generate a set of visually distinct colors.
 
         Args:
diff --git a/tiatoolbox/wsicore/wsireader.py b/tiatoolbox/wsicore/wsireader.py
index f6532cd7d..b91afdbaf 100644
--- a/tiatoolbox/wsicore/wsireader.py
+++ b/tiatoolbox/wsicore/wsireader.py
@@ -4095,7 +4095,7 @@ def read_rect(
             level_read_location,
             level_read_size,
             post_read_scale,
-            baseline_read_size,
+            _,
         ) = self.find_read_rect_params(
             location=location,
             size=size,

From 4972332f88f682ef3dd2a27e511c13337d024403 Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Mon, 24 Jun 2024 15:52:48 +0100
Subject: [PATCH 05/36] make .tif be recognised same as .tiff

---
 tiatoolbox/visualization/bokeh_app/main.py | 1 +
 tiatoolbox/wsicore/wsireader.py            | 4 +++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index b58ae529e..4e6c04d3c 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -2099,6 +2099,7 @@ def setup_doc(self: DocConfig, base_doc: Document) -> tuple[Row, Tabs]:
             "*.svs",
             "*.ndpi",
             "*.tiff",
+            "*.tif",
             "*.mrxs",
             "*.png",
             "*.jpg",
diff --git a/tiatoolbox/wsicore/wsireader.py b/tiatoolbox/wsicore/wsireader.py
index b91afdbaf..3f6cc95dd 100644
--- a/tiatoolbox/wsicore/wsireader.py
+++ b/tiatoolbox/wsicore/wsireader.py
@@ -400,7 +400,9 @@ def open(  # noqa: PLR0911
                 )
             return NGFFWSIReader(input_path, mpp=mpp, power=power)
 
-        if suffixes[-2:] in ([".ome", ".tiff"],):
+        if suffixes[-2:] in ([".ome", ".tiff"],) or suffixes[-2:] in (
+            [".ome", ".tif"],
+        ):
             return TIFFWSIReader(input_path, mpp=mpp, power=power, post_proc=post_proc)
 
         if last_suffix == ".qptiff":

From dccf4db6ae81f88a886984111f6d5a450c88aaf7 Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Wed, 26 Jun 2024 02:53:39 +0100
Subject: [PATCH 06/36] fix read_rect

---
 tiatoolbox/visualization/bokeh_app/main.py |  2 +-
 tiatoolbox/wsicore/wsireader.py            | 40 +++++++++++++++-------
 2 files changed, 28 insertions(+), 14 deletions(-)

diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index bdd612e3a..0bfa55fb4 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -2086,7 +2086,7 @@ def setup_doc(self: DocConfig, base_doc: Document) -> tuple[Row, Tabs]:
 
         # Set initial slide to first one in base folder
         slide_list = []
-        for ext in ["*.svs", "*ndpi", "*.tiff", "*.mrxs", "*.png", "*.jpg"]:
+        for ext in ["*.svs", "*ndpi", "*.tiff", "*.tif", "*.mrxs", "*.png", "*.jpg"]:
             slide_list.extend(list(doc_config["slide_folder"].glob(ext)))
             slide_list.extend(
                 list(doc_config["slide_folder"].glob(str(Path("*") / ext))),
diff --git a/tiatoolbox/wsicore/wsireader.py b/tiatoolbox/wsicore/wsireader.py
index dc55ddc3c..82915eaad 100644
--- a/tiatoolbox/wsicore/wsireader.py
+++ b/tiatoolbox/wsicore/wsireader.py
@@ -2,7 +2,6 @@
 
 from __future__ import annotations
 
-import copy
 import json
 import logging
 import math
@@ -380,7 +379,9 @@ def open(  # noqa: PLR0911
                 )
             return NGFFWSIReader(input_path, mpp=mpp, power=power)
 
-        if suffixes[-2:] in ([".ome", ".tiff"],):
+        if suffixes[-2:] in ([".ome", ".tiff"],) or suffixes[-2:] in (
+            [".ome", ".tif"],
+        ):
             return TIFFWSIReader(input_path, mpp=mpp, power=power)
 
         if last_suffix in (".tif", ".tiff"):
@@ -477,7 +478,7 @@ def info(self: WSIReader) -> WSIMeta:
 
         """
         if self._m_info is not None:
-            return copy.deepcopy(self._m_info)
+            return self._m_info
         self._m_info = self._info()
         if self._manual_mpp:
             self._m_info.mpp = np.array(self._manual_mpp)
@@ -3472,7 +3473,14 @@ def __init__(
                 len(self.tiff.pages) == 1,
             ],
         )
-        if not any([self.tiff.is_svs, self.tiff.is_ome, is_single_page_tiled]):
+        if not any(
+            [
+                self.tiff.is_svs,
+                self.tiff.is_ome,
+                is_single_page_tiled,
+                self.tiff.is_bigtiff,
+            ]
+        ):
             msg = "Unsupported TIFF WSI format."
             raise ValueError(msg)
 
@@ -3503,9 +3511,16 @@ def page_area(page: tifffile.TiffPage) -> float:
             group[0] = self._zarr_group
             self._zarr_group = group
         self.level_arrays = {
-            int(key): ArrayView(array, axes=self.info.axes)
+            int(key): ArrayView(array, axes=self._axes)
             for key, array in self._zarr_group.items()
         }
+        # ensure level arrays are sorted by descending area
+        self.level_arrays = dict(
+            sorted(
+                self.level_arrays.items(),
+                key=lambda x: -np.prod(self._canonical_shape(x[1].array.shape[:2])),
+            )
+        )
 
     def _canonical_shape(self: TIFFWSIReader, shape: IntPair) -> tuple:
         """Make a level shape tuple in YXS order.
@@ -3761,10 +3776,10 @@ def _info(self: TIFFWSIReader) -> WSIMeta:
                 Containing metadata.
 
         """
-        level_count = len(self._zarr_group)
+        level_count = len(self.level_arrays)
         level_dimensions = [
-            np.array(self._canonical_shape(p.shape)[:2][::-1])
-            for p in self._zarr_group.values()
+            np.array(self._canonical_shape(p.array.shape)[:2][::-1])
+            for p in self.level_arrays.values()
         ]
         slide_dimensions = level_dimensions[0]
         level_downsamples = [(level_dimensions[0] / x)[0] for x in level_dimensions]
@@ -4007,8 +4022,8 @@ def read_rect(
         # Find parameters for optimal read
         (
             read_level,
-            _,
-            _,
+            level_read_location,
+            level_read_size,
             post_read_scale,
             baseline_read_size,
         ) = self.find_read_rect_params(
@@ -4019,8 +4034,8 @@ def read_rect(
         )
 
         bounds = utils.transforms.locsize2bounds(
-            location=location,
-            size=baseline_read_size,
+            location=level_read_location,
+            size=level_read_size,
         )
         im_region = utils.image.safe_padded_read(
             image=self.level_arrays[read_level],
@@ -4028,7 +4043,6 @@ def read_rect(
             pad_mode=pad_mode,
             pad_constant_values=pad_constant_values,
         )
-
         im_region = utils.transforms.imresize(
             img=im_region,
             scale_factor=post_read_scale,

From 79dcd51931aa86537cbba105ab3d27a4b8443b4a Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Wed, 26 Jun 2024 22:20:05 +0100
Subject: [PATCH 07/36] fix typo

---
 tests/test_wsireader.py           | 1 +
 tiatoolbox/utils/postproc_defs.py | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/test_wsireader.py b/tests/test_wsireader.py
index c6bb6e3d9..e8d0f28da 100644
--- a/tests/test_wsireader.py
+++ b/tests/test_wsireader.py
@@ -2663,6 +2663,7 @@ def test_read_rect_level_consistency(wsi: WSIReader) -> None:
     # adds some tolerance for the comparison.
     blurred = [cv2.GaussianBlur(img, (5, 5), cv2.BORDER_REFLECT) for img in resized]
     as_float = [img.astype(np.float64) for img in blurred]
+
     # Pair-wise check resolutions for mean squared error
     for i, a in enumerate(as_float):
         for b in as_float[i + 1 :]:
diff --git a/tiatoolbox/utils/postproc_defs.py b/tiatoolbox/utils/postproc_defs.py
index ee56f5dd9..28170a132 100644
--- a/tiatoolbox/utils/postproc_defs.py
+++ b/tiatoolbox/utils/postproc_defs.py
@@ -23,7 +23,7 @@ def __init__(
         """
         self.colors = colors
         if self.colors is not None:
-            self.colors = np.array(self.default_colors, dtype=np.float32)
+            self.colors = np.array(self.colors, dtype=np.float32)
 
     @staticmethod
     def generate_colors(n_channels: int) -> np.ndarray:

From a80655b4200f30d1a58a6666777ad49f176e4dfd Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Tue, 2 Jul 2024 01:30:17 +0100
Subject: [PATCH 08/36] get colors from metadata if poss.

---
 tiatoolbox/utils/postproc_defs.py | 26 +++++++++++++++-----------
 tiatoolbox/wsicore/wsireader.py   | 31 +++++++++++++++++++++++++++++++
 2 files changed, 46 insertions(+), 11 deletions(-)

diff --git a/tiatoolbox/utils/postproc_defs.py b/tiatoolbox/utils/postproc_defs.py
index 28170a132..427824574 100644
--- a/tiatoolbox/utils/postproc_defs.py
+++ b/tiatoolbox/utils/postproc_defs.py
@@ -12,21 +12,18 @@ class MultichannelToRGB:
 
     def __init__(
         self: MultichannelToRGB,
-        colors: list[tuple[float, float, float]] | None = None,
+        color_dict: list[tuple[float, float, float]] | None = None,
     ) -> None:
         """Initialize the MultichannelToRGB converter.
 
         Args:
-            colors: List of RGB colors for each channel. If not
+            color_dict: Dict of channel names with RGB colors for each channel. If not
             provided, a set of distinct colors will be auto-generated.
 
         """
-        self.colors = colors
-        if self.colors is not None:
-            self.colors = np.array(self.colors, dtype=np.float32)
+        self.color_dict = color_dict
 
-    @staticmethod
-    def generate_colors(n_channels: int) -> np.ndarray:
+    def generate_colors(self: MultichannelToRGB, n_channels: int) -> np.ndarray:
         """Generate a set of visually distinct colors.
 
         Args:
@@ -36,10 +33,10 @@ def generate_colors(n_channels: int) -> np.ndarray:
             np.ndarray: Array of RGB colors
 
         """
-        return np.array(
-            [colorsys.hsv_to_rgb(i / n_channels, 1, 1) for i in range(n_channels)],
-            dtype=np.float32,
-        )
+        self.color_dict = {
+            f"channel_{i}": colorsys.hsv_to_rgb(i / n_channels, 1, 1)
+            for i in range(n_channels)
+        }
 
     def __call__(self: MultichannelToRGB, image: np.ndarray) -> np.ndarray:
         """Convert a multi-channel image to an RGB image.
@@ -65,3 +62,10 @@ def __call__(self: MultichannelToRGB, image: np.ndarray) -> np.ndarray:
 
         # Clip  to ensure in valid range and return
         return np.clip(rgb_image, 0, 255).astype(np.uint8)
+
+    def __setattr__(self: MultichannelToRGB, name: str, value: np.Any) -> None:
+        """Ensure that colors is updated if color_dict is updated."""
+        if name == "color_dict" and value is not None:
+            self.colors = np.array(list(value.values()), dtype=np.float32)
+
+        super().__setattr__(name, value)
diff --git a/tiatoolbox/wsicore/wsireader.py b/tiatoolbox/wsicore/wsireader.py
index 26a914e70..810a5b320 100644
--- a/tiatoolbox/wsicore/wsireader.py
+++ b/tiatoolbox/wsicore/wsireader.py
@@ -12,6 +12,7 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
+import matplotlib.colors as mcolors
 import numpy as np
 import openslide
 import pandas as pd
@@ -3597,6 +3598,36 @@ def page_area(page: tifffile.TiffPage) -> float:
                 key=lambda x: -np.prod(self._canonical_shape(x[1].array.shape[:2])),
             )
         )
+        # maybe get colors if they exist in metadata
+        self._get_colors_from_meta()
+
+    def _get_colors_from_meta(self: TIFFWSIReader) -> None:
+        """Get colors from metadata if they exist."""
+        if isinstance(self.post_proc, postproc_defs.MultichannelToRGB):
+            xml = self.info.raw["Description"]
+            try:
+                root = ElementTree.fromstring(xml)
+            except ElementTree.ParseError:
+                return
+            color_info = root.find(".//ScanColorTable")
+            if color_info is not None:
+                color_dict = {
+                    k.text.split("_")[0]: v.text
+                    for k, v in zip(
+                        color_info.iterfind("ScanColorTable-k"),
+                        color_info.iterfind("ScanColorTable-v"),
+                    )
+                }
+                # values will be either a string of 3 ints e.g 155, 128, 0, or
+                # a color name e.g Lime. Convert them all to RGB tuples.
+                for key, value in color_dict.items():
+                    if value is None:
+                        continue
+                    if "," in value:
+                        color_dict[key] = tuple(int(x) / 255 for x in value.split(","))
+                    else:
+                        color_dict[key] = mcolors.to_rgb(value)
+                self.post_proc.color_dict = color_dict
 
     def _canonical_shape(self: TIFFWSIReader, shape: IntPair) -> tuple:
         """Make a level shape tuple in YXS order.

From 83c695469fbd9a61d381a3ab6ed82473ccf3c1fe Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Tue, 2 Jul 2024 16:47:50 +0100
Subject: [PATCH 09/36] deepsource

---
 tiatoolbox/utils/postproc_defs.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tiatoolbox/utils/postproc_defs.py b/tiatoolbox/utils/postproc_defs.py
index 427824574..ee7dd413d 100644
--- a/tiatoolbox/utils/postproc_defs.py
+++ b/tiatoolbox/utils/postproc_defs.py
@@ -21,6 +21,7 @@ def __init__(
             provided, a set of distinct colors will be auto-generated.
 
         """
+        self.colors = None
         self.color_dict = color_dict
 
     def generate_colors(self: MultichannelToRGB, n_channels: int) -> np.ndarray:
@@ -55,7 +56,7 @@ def __call__(self: MultichannelToRGB, image: np.ndarray) -> np.ndarray:
             return image
 
         if self.colors is None:
-            self.colors = self.generate_colors(n)
+            self.generate_colors(n)
 
         # Convert to RGB image
         rgb_image = np.einsum("hwn,nc->hwc", image, self.colors, optimize=True)

From 6e58ec51c13ea0ae0549b635144d5a1ca08a584d Mon Sep 17 00:00:00 2001
From: behnazelhaminia <behnazelhaminia@yahoo.com>
Date: Fri, 5 Jul 2024 10:12:54 +0100
Subject: [PATCH 10/36] :white_check_mark: Adding test for mutli_channel
 visualisation

---
 tests/test_wsireader.py           | 17 +++++++++++++++--
 tiatoolbox/utils/postproc_defs.py |  4 +++-
 tiatoolbox/wsicore/wsireader.py   |  4 ++--
 3 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/tests/test_wsireader.py b/tests/test_wsireader.py
index e8d0f28da..9d472502e 100644
--- a/tests/test_wsireader.py
+++ b/tests/test_wsireader.py
@@ -211,7 +211,7 @@ def read_bounds_level_consistency(wsi: WSIReader, bounds: IntBounds) -> None:
 
     # Pair-wise check resolutions for mean squared error
     for i, a in enumerate(as_float):
-        for b in as_float[i + 1 :]:
+        for b in as_float[i + 1:]:
             _, error, phase_diff = phase_cross_correlation(a, b, normalization=None)
             assert phase_diff < 0.125
             assert error < 0.125
@@ -2666,7 +2666,7 @@ def test_read_rect_level_consistency(wsi: WSIReader) -> None:
 
     # Pair-wise check resolutions for mean squared error
     for i, a in enumerate(as_float):
-        for b in as_float[i + 1 :]:
+        for b in as_float[i + 1:]:
             _, error, phase_diff = phase_cross_correlation(a, b, normalization=None)
             assert phase_diff < 0.125
             assert error < 0.125
@@ -2804,3 +2804,16 @@ def test_read_multi_channel(source_image: Path) -> None:
     assert region.shape == (100, 50, (new_img_array.shape[-1]))
     assert np.abs(np.median(region.astype(int) - target.astype(int))) == 0
     assert np.abs(np.mean(region.astype(int) - target.astype(int))) < 0.2
+
+
+def test_visualise_multi_channel(sample_qptiff: Path) -> None:
+    """Test visualising a multi-channel qptiff image"""
+
+    wsi = wsireader.TIFFWSIReader(sample_qptiff, post_proc='auto')
+    wsi2 = wsireader.TIFFWSIReader(sample_qptiff, post_proc=None)
+
+    region = wsi.read_rect(location=(0, 0), size=(50, 100))
+    region2 = wsi2.read_rect(location=(0, 0), size=(50, 100))
+
+    assert region.shape == (100, 50, 3)
+    assert region2.shape == (100, 50, 7)
diff --git a/tiatoolbox/utils/postproc_defs.py b/tiatoolbox/utils/postproc_defs.py
index ee7dd413d..b7e3aa5c9 100644
--- a/tiatoolbox/utils/postproc_defs.py
+++ b/tiatoolbox/utils/postproc_defs.py
@@ -50,6 +50,8 @@ def __call__(self: MultichannelToRGB, image: np.ndarray) -> np.ndarray:
 
         """
         n = image.shape[2]
+        print(n)
+        print(self.color_dict)
 
         if n < 5:  # noqa: PLR2004
             # assume already rgb(a) so just return image
@@ -59,7 +61,7 @@ def __call__(self: MultichannelToRGB, image: np.ndarray) -> np.ndarray:
             self.generate_colors(n)
 
         # Convert to RGB image
-        rgb_image = np.einsum("hwn,nc->hwc", image, self.colors, optimize=True)
+        rgb_image = np.einsum("hwn,nc->hwc", image, self.colors[:, :], optimize=True)
 
         # Clip  to ensure in valid range and return
         return np.clip(rgb_image, 0, 255).astype(np.uint8)
diff --git a/tiatoolbox/wsicore/wsireader.py b/tiatoolbox/wsicore/wsireader.py
index 810a5b320..fb858dae3 100644
--- a/tiatoolbox/wsicore/wsireader.py
+++ b/tiatoolbox/wsicore/wsireader.py
@@ -4126,7 +4126,7 @@ def read_rect(
             )
             if self.post_proc is not None:
                 im_region = self.post_proc(im_region)
-            return utils.transforms.background_composite(im_region, alpha=False)
+            return im_region
 
         # Find parameters for optimal read
         (
@@ -4161,7 +4161,7 @@ def read_rect(
 
         if self.post_proc is not None:
             im_region = self.post_proc(im_region)
-        return utils.transforms.background_composite(image=im_region, alpha=False)
+        return im_region
 
     def read_bounds(
         self: TIFFWSIReader,

From c4e4232ac817a48e4c227539a7b684a36fea4833 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 5 Jul 2024 09:16:16 +0000
Subject: [PATCH 11/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/test_wsireader.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tests/test_wsireader.py b/tests/test_wsireader.py
index 9d472502e..cc9d3157b 100644
--- a/tests/test_wsireader.py
+++ b/tests/test_wsireader.py
@@ -211,7 +211,7 @@ def read_bounds_level_consistency(wsi: WSIReader, bounds: IntBounds) -> None:
 
     # Pair-wise check resolutions for mean squared error
     for i, a in enumerate(as_float):
-        for b in as_float[i + 1:]:
+        for b in as_float[i + 1 :]:
             _, error, phase_diff = phase_cross_correlation(a, b, normalization=None)
             assert phase_diff < 0.125
             assert error < 0.125
@@ -2666,7 +2666,7 @@ def test_read_rect_level_consistency(wsi: WSIReader) -> None:
 
     # Pair-wise check resolutions for mean squared error
     for i, a in enumerate(as_float):
-        for b in as_float[i + 1:]:
+        for b in as_float[i + 1 :]:
             _, error, phase_diff = phase_cross_correlation(a, b, normalization=None)
             assert phase_diff < 0.125
             assert error < 0.125
@@ -2808,8 +2808,7 @@ def test_read_multi_channel(source_image: Path) -> None:
 
 def test_visualise_multi_channel(sample_qptiff: Path) -> None:
     """Test visualising a multi-channel qptiff image"""
-
-    wsi = wsireader.TIFFWSIReader(sample_qptiff, post_proc='auto')
+    wsi = wsireader.TIFFWSIReader(sample_qptiff, post_proc="auto")
     wsi2 = wsireader.TIFFWSIReader(sample_qptiff, post_proc=None)
 
     region = wsi.read_rect(location=(0, 0), size=(50, 100))

From 5563e36d7e6e2ac5cd633fbcbc411271fd0f57c4 Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Fri, 5 Jul 2024 11:06:57 +0100
Subject: [PATCH 12/36] replace depreciated funcTickFormatter

---
 tiatoolbox/visualization/bokeh_app/main.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index 4e6c04d3c..38c581987 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -14,6 +14,10 @@
 import numpy as np
 import requests
 import torch
+from matplotlib import colormaps
+from PIL import Image
+from requests.adapters import HTTPAdapter, Retry
+
 from bokeh.events import ButtonClick, DoubleTap, MenuItemClick
 from bokeh.io import curdoc
 from bokeh.layouts import column, row
@@ -28,10 +32,10 @@
     Column,
     ColumnDataSource,
     CustomJS,
+    CustomJSTickFormatter,
     DataTable,
     Div,
     Dropdown,
-    FuncTickFormatter,
     Glyph,
     HoverTool,
     HTMLTemplateFormatter,
@@ -58,9 +62,6 @@
 from bokeh.models.tiles import WMTSTileSource
 from bokeh.plotting import figure
 from bokeh.util import token
-from matplotlib import colormaps
-from PIL import Image
-from requests.adapters import HTTPAdapter, Retry
 
 # GitHub actions seems unable to find TIAToolbox unless this is here
 sys.path.insert(0, str(Path(__file__).parent.parent.parent.parent))
@@ -630,7 +631,7 @@ def __init__(self: ViewerState, slide_path: str | Path) -> None:
         self.thickness = -1
         self.model_mpp = 0
         self.init = True
-        self.micron_formatter = FuncTickFormatter(
+        self.micron_formatter = CustomJSTickFormatter(
             args={"mpp": 0.1},
             code="""
                 return Math.round(tick*mpp)

From cc66c5305d399a6b677d79b6b38b22336a7751a3 Mon Sep 17 00:00:00 2001
From: behnazelhaminia <behnazelhaminia@yahoo.com>
Date: Fri, 5 Jul 2024 12:46:55 +0100
Subject: [PATCH 13/36] :white_check_mark: Adding test for mutli_channel
 visualisation

---
 tests/test_wsireader.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/tests/test_wsireader.py b/tests/test_wsireader.py
index 9d472502e..35f1b8935 100644
--- a/tests/test_wsireader.py
+++ b/tests/test_wsireader.py
@@ -211,7 +211,7 @@ def read_bounds_level_consistency(wsi: WSIReader, bounds: IntBounds) -> None:
 
     # Pair-wise check resolutions for mean squared error
     for i, a in enumerate(as_float):
-        for b in as_float[i + 1:]:
+        for b in as_float[i + 1 :]:
             _, error, phase_diff = phase_cross_correlation(a, b, normalization=None)
             assert phase_diff < 0.125
             assert error < 0.125
@@ -2666,7 +2666,7 @@ def test_read_rect_level_consistency(wsi: WSIReader) -> None:
 
     # Pair-wise check resolutions for mean squared error
     for i, a in enumerate(as_float):
-        for b in as_float[i + 1:]:
+        for b in as_float[i + 1 :]:
             _, error, phase_diff = phase_cross_correlation(a, b, normalization=None)
             assert phase_diff < 0.125
             assert error < 0.125
@@ -2807,9 +2807,8 @@ def test_read_multi_channel(source_image: Path) -> None:
 
 
 def test_visualise_multi_channel(sample_qptiff: Path) -> None:
-    """Test visualising a multi-channel qptiff image"""
-
-    wsi = wsireader.TIFFWSIReader(sample_qptiff, post_proc='auto')
+    """Test visualising a multi-channel qptiff image."""
+    wsi = wsireader.TIFFWSIReader(sample_qptiff, post_proc="auto")
     wsi2 = wsireader.TIFFWSIReader(sample_qptiff, post_proc=None)
 
     region = wsi.read_rect(location=(0, 0), size=(50, 100))

From 7f4423c58ce99c1fc16b27e6fc54f2f4acf2781c Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Wed, 7 Aug 2024 15:11:36 +0100
Subject: [PATCH 14/36] drop background autofluorescence channel if appropriate

---
 tiatoolbox/utils/postproc_defs.py | 37 +++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/tiatoolbox/utils/postproc_defs.py b/tiatoolbox/utils/postproc_defs.py
index ee7dd413d..e41e3517c 100644
--- a/tiatoolbox/utils/postproc_defs.py
+++ b/tiatoolbox/utils/postproc_defs.py
@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import colorsys
+import warnings
 
 import numpy as np
 
@@ -23,6 +24,39 @@ def __init__(
         """
         self.colors = None
         self.color_dict = color_dict
+        self.is_validated = False
+
+    def validate(self: MultichannelToRGB, n: int) -> None:
+        """Validate the input color_dict on first read from image.
+
+        Checks that n is either equal to the number of colors provided, or is
+        one less. In the latter case it is assumed that the last channel is background
+        autofluorescence and is not in the tiff and we will drop it from
+        the color_dict with a warning.
+
+        Args:
+            n (int): Number of channels
+
+        """
+        n_colors = len(self.color_dict)
+        if n_colors == n:
+            self.is_validated = True
+            return
+
+        if n_colors - 1 == n:
+            self.color_dict.pop(list(self.color_dict.keys())[-1])
+            self.colors = self.colors[:-1]
+            self.is_validated = True
+            warnings.warn(
+                """Number of channels in image is one less than number of channels in
+                dict. Assuming last channel is background autofluorescence and dropping
+                it. If this is not the case please provide a manual color_dict.""",
+                stacklevel=2,
+            )
+            return
+
+        msg = f"Number of colors: {n_colors} does not match channels in image: {n}."
+        raise ValueError(msg)
 
     def generate_colors(self: MultichannelToRGB, n_channels: int) -> np.ndarray:
         """Generate a set of visually distinct colors.
@@ -58,6 +92,9 @@ def __call__(self: MultichannelToRGB, image: np.ndarray) -> np.ndarray:
         if self.colors is None:
             self.generate_colors(n)
 
+        if not self.is_validated:
+            self.validate(n)
+
         # Convert to RGB image
         rgb_image = np.einsum("hwn,nc->hwc", image, self.colors, optimize=True)
 

From 8e2c11ae871e40bd46f63e589b23983a7f57bd7e Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Wed, 7 Aug 2024 16:01:24 +0100
Subject: [PATCH 15/36] remove a print

---
 tiatoolbox/utils/postproc_defs.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tiatoolbox/utils/postproc_defs.py b/tiatoolbox/utils/postproc_defs.py
index c35452a81..e4ee3174c 100644
--- a/tiatoolbox/utils/postproc_defs.py
+++ b/tiatoolbox/utils/postproc_defs.py
@@ -84,8 +84,6 @@ def __call__(self: MultichannelToRGB, image: np.ndarray) -> np.ndarray:
 
         """
         n = image.shape[2]
-        print(n)
-        print(self.color_dict)
 
         if n < 5:  # noqa: PLR2004
             # assume already rgb(a) so just return image

From fad00c334744b8a3ee3ae0a7a1925ed96a115d4f Mon Sep 17 00:00:00 2001
From: Behnaz <behnazelhaminia@yahoo.com>
Date: Fri, 9 Aug 2024 14:46:33 +0100
Subject: [PATCH 16/36] :white_check_mark: Assert shape and interpolation

---
 tests/test_wsireader.py             | 22 ++++++++++++++++++++++
 tiatoolbox/data/remote_samples.yaml |  2 ++
 2 files changed, 24 insertions(+)

diff --git a/tests/test_wsireader.py b/tests/test_wsireader.py
index e8d0f28da..108038e26 100644
--- a/tests/test_wsireader.py
+++ b/tests/test_wsireader.py
@@ -1474,6 +1474,7 @@ def test_wsireader_open(
     sample_ome_tiff: Path,
     sample_ventana_tif: Path,
     sample_regular_tif: Path,
+    sample_qptiff: Path,
     source_image: Path,
     tmp_path: pytest.TempPathFactory,
 ) -> None:
@@ -1505,6 +1506,9 @@ def test_wsireader_open(
     wsi = WSIReader.open(Path(source_image))
     assert isinstance(wsi, wsireader.VirtualWSIReader)
 
+    wsi = WSIReader.open(sample_qptiff)
+    assert isinstance(wsi, wsireader.TIFFWSIReader)
+
     img = utils.misc.imread(str(Path(source_image)))
     wsi = WSIReader.open(input_img=img)
     assert isinstance(wsi, wsireader.VirtualWSIReader)
@@ -2573,6 +2577,11 @@ def test_jp2_no_header(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
             "sample_key": "jp2-omnyx-small",
             "kwargs": {},
         },
+        {
+            "reader_class": TIFFWSIReader,
+            "sample_key": "qptiff_sample",
+            "kwargs": {},
+        },
     ],
     ids=[
         "AnnotationReaderOverlaid",
@@ -2804,3 +2813,16 @@ def test_read_multi_channel(source_image: Path) -> None:
     assert region.shape == (100, 50, (new_img_array.shape[-1]))
     assert np.abs(np.median(region.astype(int) - target.astype(int))) == 0
     assert np.abs(np.mean(region.astype(int) - target.astype(int))) < 0.2
+
+
+def test_visualise_multi_channel(sample_qptiff: Path) -> None:
+    """Test visualising a multi-channel qptiff image."""
+    wsi = wsireader.TIFFWSIReader(sample_qptiff, post_proc="auto")
+    wsi2 = wsireader.TIFFWSIReader(sample_qptiff, post_proc=None)
+
+    region = wsi.read_rect(location=(0, 0), size=(50, 100))
+    region2 = wsi2.read_rect(location=(0, 0), size=(50, 100))
+
+    assert region.shape == (100, 50, 3)
+    assert region2.shape == (100, 50, 7)
+
diff --git a/tiatoolbox/data/remote_samples.yaml b/tiatoolbox/data/remote_samples.yaml
index 58fff49d3..75e5fccf7 100644
--- a/tiatoolbox/data/remote_samples.yaml
+++ b/tiatoolbox/data/remote_samples.yaml
@@ -143,3 +143,5 @@ files:
     url: [ *testdata, "annotation/test2_config.json"]
   nuclick-output:
     url: [*modelroot, "predictions/nuclei_mask/nuclick-output.npy"]
+  qptiff_sample:
+    url: [*wsis, "multiplexed_example.qptiff"]

From 464a5a2116684f5a5be55989f3bbb7cb717fced0 Mon Sep 17 00:00:00 2001
From: Behnaz <behnazelhaminia@yahoo.com>
Date: Fri, 9 Aug 2024 14:51:07 +0100
Subject: [PATCH 17/36] :white_check_mark: Test for multichannel visualisation

---
 tests/test_wsireader.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_wsireader.py b/tests/test_wsireader.py
index 108038e26..989d0c7d8 100644
--- a/tests/test_wsireader.py
+++ b/tests/test_wsireader.py
@@ -2825,4 +2825,3 @@ def test_visualise_multi_channel(sample_qptiff: Path) -> None:
 
     assert region.shape == (100, 50, 3)
     assert region2.shape == (100, 50, 7)
-

From 75bbdbdc0a7beb1153581981f03ef8f80344ac18 Mon Sep 17 00:00:00 2001
From: Behnaz <behnazelhaminia@yahoo.com>
Date: Fri, 9 Aug 2024 15:04:24 +0100
Subject: [PATCH 18/36] :white_check_mark: Test for multichannel visualisation

---
 tests/test_wsireader.py             | 2 +-
 tiatoolbox/data/remote_samples.yaml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_wsireader.py b/tests/test_wsireader.py
index 802f28543..137f6c1c6 100644
--- a/tests/test_wsireader.py
+++ b/tests/test_wsireader.py
@@ -2824,7 +2824,7 @@ def test_read_multi_channel(source_image: Path) -> None:
 
 
 def test_visualise_multi_channel(sample_qptiff: Path) -> None:
-    """Test visualising a multi-channel qptiff image."""
+    """Test visualising a multi-channel qptiff multiplex image."""
     wsi = wsireader.TIFFWSIReader(sample_qptiff, post_proc="auto")
     wsi2 = wsireader.TIFFWSIReader(sample_qptiff, post_proc=None)
 
diff --git a/tiatoolbox/data/remote_samples.yaml b/tiatoolbox/data/remote_samples.yaml
index 5182c87a4..aa23b8353 100644
--- a/tiatoolbox/data/remote_samples.yaml
+++ b/tiatoolbox/data/remote_samples.yaml
@@ -146,4 +146,4 @@ files:
   nuclick-output:
     url: [*modelroot, "predictions/nuclei_mask/nuclick-output.npy"]
   qptiff_sample:
-    url: [*wsis, "multiplexed_example.qptiff"]
+    url: [*wsis, "multiplexed_example.qptif"]

From b148ed38e4d010d225edc68314cea8472a6f393a Mon Sep 17 00:00:00 2001
From: behnazelhaminia <30952176+behnazelhaminia@users.noreply.github.com>
Date: Fri, 9 Aug 2024 15:05:41 +0100
Subject: [PATCH 19/36] Update remote_samples.yaml

---
 tiatoolbox/data/remote_samples.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tiatoolbox/data/remote_samples.yaml b/tiatoolbox/data/remote_samples.yaml
index aa23b8353..5182c87a4 100644
--- a/tiatoolbox/data/remote_samples.yaml
+++ b/tiatoolbox/data/remote_samples.yaml
@@ -146,4 +146,4 @@ files:
   nuclick-output:
     url: [*modelroot, "predictions/nuclei_mask/nuclick-output.npy"]
   qptiff_sample:
-    url: [*wsis, "multiplexed_example.qptif"]
+    url: [*wsis, "multiplexed_example.qptiff"]

From 93ed2d1e386b068c34029c46f94204c2ca68c5e2 Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Wed, 21 Aug 2024 20:17:00 +0100
Subject: [PATCH 20/36] first channel selector draft

---
 tiatoolbox/visualization/bokeh_app/main.py | 130 +++++++++++++++++++++
 tiatoolbox/visualization/tileserver.py     |  14 +++
 2 files changed, 144 insertions(+)

diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index 7439262d8..ea911ebe8 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -22,6 +22,7 @@
     BoxEditTool,
     Button,
     CheckboxButtonGroup,
+    CheckboxEditor,
     Circle,
     ColorBar,
     ColorPicker,
@@ -46,6 +47,7 @@
     Select,
     Slider,
     Spinner,
+    StringEditor,
     TableColumn,
     TabPanel,
     Tabs,
@@ -137,6 +139,131 @@ def format_info(info: dict[str, Any]) -> str:
     return info_str
 
 
+def get_color_dictionary() -> dict[str, tuple[int, int, int]]:
+    """Get the colors for the channels."""
+    resp = UI["s"].get(f"http://{host2}:5000/tileserver/channels")
+    try:
+        return json.loads(resp.text)
+    except json.JSONDecodeError:
+        return {}
+
+
+def set_color_dictionary(colors: dict[str, tuple[int, int, int]]) -> None:
+    """Set the colors for the channels."""
+    UI["s"].put(f"http://{host2}:5000/tileserver/channels", data=json.dumps(colors))
+
+
+def set_active_channels(active_channels: list[str]) -> None:
+    """Set the active channels in the image."""
+    UI["s"].put(
+        f"http://{host2}:5000/tileserver/active_channels",
+        data=json.dumps(active_channels),
+    )
+
+
+def get_active_channels() -> list[str]:
+    """Get the active channels in the image."""
+    return [f"channel{i}" for i in range(1, 11)]
+
+
+def create_channel_color_ui() -> Column:
+    """Create the channel select/color management UI."""
+    # Start with an empty ColumnDataSource
+    source = ColumnDataSource(data={"channels": [], "colors": [], "active": []})
+
+    # Custom formatter for the color column
+    color_formatter = HTMLTemplateFormatter(
+        template="""<div style="background-color: <%= value %>;
+          color: <%= value %>; border: 1px solid #ddd;"><%= value %></div>"""
+    )
+
+    columns = [
+        TableColumn(
+            field="channels", title="Channel", editor=StringEditor(), sortable=False
+        ),
+        TableColumn(
+            field="colors",
+            title="Color",
+            editor=StringEditor(),
+            formatter=color_formatter,
+            sortable=False,
+        ),
+        TableColumn(
+            field="active", title="Active", editor=CheckboxEditor(), sortable=False
+        ),
+    ]
+    data_table = DataTable(
+        source=source, columns=columns, editable=True, width=400, height=400
+    )
+
+    color_picker = ColorPicker(title="Selected Channel Color", width=100)
+
+    def update_selected_color(attr: str, old: str, new: str) -> None:  # noqa: ARG001
+        """Channel color picker callback."""
+        selected = source.selected.indices
+        if selected:
+            source.patch({"colors": [(selected[0], new)]})
+
+    color_picker.on_change("color", update_selected_color)
+
+    apply_button = Button(label="Apply Changes", button_type="success")
+
+    def apply_changes() -> None:
+        """Apply the changes to the image."""
+        data = source.data
+        colors = dict(zip(data["channels"], data["colors"]))
+        active_channels = [
+            channel
+            for channel, is_active in zip(data["channels"], data["active"])
+            if is_active
+        ]
+
+        set_color_dictionary(colors)
+        set_active_channels(active_channels)
+
+    apply_button.on_click(apply_changes)
+
+    def update_color_picker(attr: str, old: str, new: str) -> None:  # noqa: ARG001
+        """Update the color picker when a new row is selected."""
+        if new:
+            selected_color = source.data["colors"][new[0]]
+            color_picker.color = selected_color
+        else:
+            color_picker.color = None
+
+    source.selected.on_change("indices", update_color_picker)
+
+    instructions = Div(
+        text="""
+        <p>Instructions:</p>
+        <ul>
+            <li>Use the table to view and edit channel properties</li>
+            <li>Click on a row to select a channel</li>
+            <li>Use the color picker to change the color of the selected channel</li>
+            <li>Check or uncheck the 'Active' column to toggle channel visibility</li>
+            <li>Click 'Apply Changes' to update the image</li>
+        </ul>
+    """
+    )
+
+    return column(instructions, row(data_table, column(color_picker, apply_button)))
+
+
+def populate_table() -> None:
+    """Populate the channel color table."""
+    # Access the ColumnDataSource from the UI dictionary
+    source = UI["channel_select"].children[1].children[0].source
+    colors = get_color_dictionary()
+    active_channels = get_active_channels()
+
+    new_data = {
+        "channels": list(colors.keys()),
+        "colors": [rgb2hex(color) for color in colors.values()],
+        "active": [channel in active_channels for channel in colors],
+    }
+    source.data = new_data
+
+
 def get_view_bounds(
     dims: tuple[float, float],
     plot_size: tuple[float, float],
@@ -876,6 +1003,7 @@ def slide_select_cb(attr: str, old: str, new: str) -> None:  # noqa: ARG001
     initialise_slide()
     fname = make_safe_name(str(slide_path))
     UI["s"].put(f"http://{host2}:5000/tileserver/slide", data={"slide_path": fname})
+    populate_table()
     change_tiles("slide")
 
     # Load the overlay and graph automatically if set in config
@@ -1652,12 +1780,14 @@ def gather_ui_elements(  # noqa: PLR0915
                 "pt_size_spinner",
                 "edge_size_spinner",
                 "res_switch",
+                "channel_select",
             ],
             [
                 opt_buttons,
                 pt_size_spinner,
                 edge_size_spinner,
                 res_switch,
+                create_channel_color_ui(),
             ],
         ),
     )
diff --git a/tiatoolbox/visualization/tileserver.py b/tiatoolbox/visualization/tileserver.py
index b0a427502..053d6e6f8 100644
--- a/tiatoolbox/visualization/tileserver.py
+++ b/tiatoolbox/visualization/tileserver.py
@@ -164,6 +164,8 @@ def __init__(  # noqa: PLR0915
         )
         self.route("/tileserver/tap_query/<x>/<y>")(self.tap_query)
         self.route("/tileserver/prop_range", methods=["PUT"])(self.prop_range)
+        self.route("/tileserver/channels", methods=["GET"])(self.get_channels)
+        self.route("/tileserver/channels", methods=["PUT"])(self.set_channels)
         self.route("/tileserver/shutdown", methods=["POST"])(self.shutdown)
 
     def _get_session_id(self: TileServer) -> str:
@@ -718,6 +720,18 @@ def prop_range(self: TileServer) -> str:
         self.renderers[session_id].score_fn = lambda x: (x - minv) / (maxv - minv)
         return "done"
 
+    def get_channels(self: TileServer) -> Response:
+        """Get the channels of the slide."""
+        session_id = self._get_session_id()
+        return jsonify(self.layers[session_id]["slide"].post_proc.color_dict)
+
+    def set_channels(self: TileServer) -> str:
+        """Set the channels of the slide."""
+        session_id = self._get_session_id()
+        channels = json.loads(request.form["channels"])
+        self.layers[session_id]["slide"].post_proc.color_dict = channels
+        return "done"
+
     @staticmethod
     def shutdown() -> None:
         """Shutdown the tileserver."""

From df5a59d1a612c3788ba7aaa7bae1c0c0fcdac364 Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Thu, 22 Aug 2024 20:50:53 +0100
Subject: [PATCH 21/36] multichannel ui update

---
 tests/test_app_bokeh.py                    |  9 +--
 tests/test_wsireader.py                    |  1 +
 tiatoolbox/cli/visualize.py                |  1 +
 tiatoolbox/utils/postproc_defs.py          | 22 +++++--
 tiatoolbox/visualization/bokeh_app/main.py | 77 +++++++++++++---------
 tiatoolbox/visualization/tileserver.py     | 27 +++++++-
 6 files changed, 94 insertions(+), 43 deletions(-)

diff --git a/tests/test_app_bokeh.py b/tests/test_app_bokeh.py
index cb99a3df3..e8eec47ec 100644
--- a/tests/test_app_bokeh.py
+++ b/tests/test_app_bokeh.py
@@ -11,19 +11,19 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-import bokeh.models as bkmodels
 import matplotlib.pyplot as plt
 import numpy as np
 import pytest
 import requests
-from bokeh.application import Application
-from bokeh.application.handlers import FunctionHandler
-from bokeh.events import ButtonClick, DoubleTap, MenuItemClick
 from flask_cors import CORS
 from matplotlib import colormaps
 from PIL import Image
 from scipy.ndimage import label
 
+import bokeh.models as bkmodels
+from bokeh.application import Application
+from bokeh.application.handlers import FunctionHandler
+from bokeh.events import ButtonClick, DoubleTap, MenuItemClick
 from tiatoolbox.data import _fetch_remote_sample
 from tiatoolbox.visualization.bokeh_app import main
 from tiatoolbox.visualization.tileserver import TileServer
@@ -138,6 +138,7 @@ def run_app() -> None:
         title="Tiatoolbox TileServer",
         layers={},
     )
+    app.json.sort_keys = False
     CORS(app, send_wildcard=True)
     app.run(host="127.0.0.1", threaded=True)
 
diff --git a/tests/test_wsireader.py b/tests/test_wsireader.py
index 137f6c1c6..63e404932 100644
--- a/tests/test_wsireader.py
+++ b/tests/test_wsireader.py
@@ -2600,6 +2600,7 @@ def test_jp2_no_header(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
         "NGFFWSIReader",
         "OpenSlideWSIReader (Small SVS)",
         "OmnyxJP2WSIReader",
+        "TIFFReader_Multichannel",
     ],
 )
 def wsi(request: requests.request, remote_sample: Callable) -> WSIReader:
diff --git a/tiatoolbox/cli/visualize.py b/tiatoolbox/cli/visualize.py
index f1edbb318..9c1bf7774 100644
--- a/tiatoolbox/cli/visualize.py
+++ b/tiatoolbox/cli/visualize.py
@@ -25,6 +25,7 @@ def run_app() -> None:
             title="Tiatoolbox TileServer",
             layers={},
         )
+        app.json.sort_keys = False
         CORS(app, send_wildcard=True)
         app.run(host="127.0.0.1", threaded=True)
 
diff --git a/tiatoolbox/utils/postproc_defs.py b/tiatoolbox/utils/postproc_defs.py
index e4ee3174c..a0954384c 100644
--- a/tiatoolbox/utils/postproc_defs.py
+++ b/tiatoolbox/utils/postproc_defs.py
@@ -25,6 +25,8 @@ def __init__(
         self.colors = None
         self.color_dict = color_dict
         self.is_validated = False
+        self.channels = None
+        self.enhance = 1.0
 
     def validate(self: MultichannelToRGB, n: int) -> None:
         """Validate the input color_dict on first read from image.
@@ -38,18 +40,18 @@ def validate(self: MultichannelToRGB, n: int) -> None:
             n (int): Number of channels
 
         """
-        n_colors = len(self.color_dict)
+        n_colors = len(self.colors)
         if n_colors == n:
             self.is_validated = True
             return
 
         if n_colors - 1 == n:
-            self.color_dict.pop(list(self.color_dict.keys())[-1])
-            self.colors = self.colors[:-1]
+            self.colors = self.colors[:n]
+            self.channels = [c for c in self.channels if c < n]
             self.is_validated = True
             warnings.warn(
                 """Number of channels in image is one less than number of channels in
-                dict. Assuming last channel is background autofluorescence and dropping
+                dict. Assuming last channel is background autofluorescence and ignoring
                 it. If this is not the case please provide a manual color_dict.""",
                 stacklevel=2,
             )
@@ -96,7 +98,15 @@ def __call__(self: MultichannelToRGB, image: np.ndarray) -> np.ndarray:
             self.validate(n)
 
         # Convert to RGB image
-        rgb_image = np.einsum("hwn,nc->hwc", image, self.colors[:, :], optimize=True)
+        rgb_image = (
+            np.einsum(
+                "hwn,nc->hwc",
+                image[:, :, self.channels],
+                self.colors[self.channels, :],
+                optimize=True,
+            )
+            * self.enhance
+        )
 
         # Clip  to ensure in valid range and return
         return np.clip(rgb_image, 0, 255).astype(np.uint8)
@@ -105,5 +115,7 @@ def __setattr__(self: MultichannelToRGB, name: str, value: np.Any) -> None:
         """Ensure that colors is updated if color_dict is updated."""
         if name == "color_dict" and value is not None:
             self.colors = np.array(list(value.values()), dtype=np.float32)
+            if self.channels is None:
+                self.channels = list(range(len(value)))
 
         super().__setattr__(name, value)
diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index 65b12a841..f679bbaf1 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -140,33 +140,26 @@ def format_info(info: dict[str, Any]) -> str:
     return info_str
 
 
-def get_color_dictionary() -> dict[str, tuple[int, int, int]]:
+def get_channel_info() -> dict[str, tuple[int, int, int]]:
     """Get the colors for the channels."""
     resp = UI["s"].get(f"http://{host2}:5000/tileserver/channels")
     try:
-        return json.loads(resp.text)
+        resp = json.loads(resp.text)
+        return resp["channels"], resp["active"]
     except json.JSONDecodeError:
-        return {}
+        return {}, []
 
 
-def set_color_dictionary(colors: dict[str, tuple[int, int, int]]) -> None:
+def set_channel_info(
+    colors: dict[str, tuple[int, int, int]], active_channels: list
+) -> None:
     """Set the colors for the channels."""
-    UI["s"].put(f"http://{host2}:5000/tileserver/channels", data=json.dumps(colors))
-
-
-def set_active_channels(active_channels: list[str]) -> None:
-    """Set the active channels in the image."""
     UI["s"].put(
-        f"http://{host2}:5000/tileserver/active_channels",
-        data=json.dumps(active_channels),
+        f"http://{host2}:5000/tileserver/channels",
+        data={"channels": json.dumps(colors), "active": json.dumps(active_channels)},
     )
 
 
-def get_active_channels() -> list[str]:
-    """Get the active channels in the image."""
-    return [f"channel{i}" for i in range(1, 11)]
-
-
 def create_channel_color_ui() -> Column:
     """Create the channel select/color management UI."""
     # Start with an empty ColumnDataSource
@@ -194,12 +187,12 @@ def create_channel_color_ui() -> Column:
         ),
     ]
     data_table = DataTable(
-        source=source, columns=columns, editable=True, width=400, height=400
+        source=source, columns=columns, editable=True, width=250, height=200
     )
 
-    color_picker = ColorPicker(title="Selected Channel Color", width=100)
+    color_picker = ColorPicker(title="Selected Color", width=100)
 
-    def update_selected_color(attr: str, old: str, new: str) -> None:  # noqa: ARG001
+    def update_selected_color(attr: str, old: str, new: str) -> None:  # noqa: ARG001 # skipcq: PYL-W0613
         """Channel color picker callback."""
         selected = source.selected.indices
         if selected:
@@ -207,24 +200,24 @@ def update_selected_color(attr: str, old: str, new: str) -> None:  # noqa: ARG00
 
     color_picker.on_change("color", update_selected_color)
 
-    apply_button = Button(label="Apply Changes", button_type="success")
+    apply_button = Button(
+        label="Apply Changes", button_type="success", margin=(20, 5, 5, 5)
+    )
 
     def apply_changes() -> None:
         """Apply the changes to the image."""
         data = source.data
         colors = dict(zip(data["channels"], data["colors"]))
         active_channels = [
-            channel
-            for channel, is_active in zip(data["channels"], data["active"])
-            if is_active
+            channel for channel, is_active in enumerate(data["active"]) if is_active
         ]
 
-        set_color_dictionary(colors)
-        set_active_channels(active_channels)
+        set_channel_info({ch: hex2rgb(colors[ch]) for ch in colors}, active_channels)
+        change_tiles("slide")
 
     apply_button.on_click(apply_changes)
 
-    def update_color_picker(attr: str, old: str, new: str) -> None:  # noqa: ARG001
+    def update_color_picker(attr: str, old: str, new: str) -> None:  # noqa: ARG001 # skipcq: PYL-W0613
         """Update the color picker when a new row is selected."""
         if new:
             selected_color = source.data["colors"][new[0]]
@@ -234,6 +227,26 @@ def update_color_picker(attr: str, old: str, new: str) -> None:  # noqa: ARG001
 
     source.selected.on_change("indices", update_color_picker)
 
+    enhance_slider = Slider(
+        start=0.1,
+        end=10,
+        value=1,
+        step=0.1,
+        title="Enhance",
+        width=200,
+    )
+
+    def enhance_cb(attr: str, old: str, new: str) -> None:  # noqa: ARG001 # skipcq: PYL-W0613
+        """Enhance slider callback."""
+        UI["s"].put(
+            f"http://{host2}:5000/tileserver/enhance",
+            data={"val": json.dumps(new)},
+        )
+        UI["vstate"].update_state = 1
+        UI["vstate"].to_update.update(["slide"])
+
+    enhance_slider.on_change("value", enhance_cb)
+
     instructions = Div(
         text="""
         <p>Instructions:</p>
@@ -247,20 +260,22 @@ def update_color_picker(attr: str, old: str, new: str) -> None:  # noqa: ARG001
     """
     )
 
-    return column(instructions, row(data_table, column(color_picker, apply_button)))
+    return column(
+        instructions,
+        column(data_table, row(color_picker, apply_button), enhance_slider),
+    )
 
 
 def populate_table() -> None:
     """Populate the channel color table."""
     # Access the ColumnDataSource from the UI dictionary
     source = UI["channel_select"].children[1].children[0].source
-    colors = get_color_dictionary()
-    active_channels = get_active_channels()
+    colors, active_channels = get_channel_info()
 
     new_data = {
         "channels": list(colors.keys()),
         "colors": [rgb2hex(color) for color in colors.values()],
-        "active": [channel in active_channels for channel in colors],
+        "active": [channel in active_channels for channel in range(len(colors))],
     }
     source.data = new_data
 
@@ -1004,8 +1019,8 @@ def slide_select_cb(attr: str, old: str, new: str) -> None:  # noqa: ARG001
     initialise_slide()
     fname = make_safe_name(str(slide_path))
     UI["s"].put(f"http://{host2}:5000/tileserver/slide", data={"slide_path": fname})
-    populate_table()
     change_tiles("slide")
+    populate_table()
 
     # Load the overlay and graph automatically if set in config
     if doc_config["auto_load"]:
diff --git a/tiatoolbox/visualization/tileserver.py b/tiatoolbox/visualization/tileserver.py
index 053d6e6f8..5b637e169 100644
--- a/tiatoolbox/visualization/tileserver.py
+++ b/tiatoolbox/visualization/tileserver.py
@@ -24,6 +24,7 @@
 from tiatoolbox.annotation import AnnotationStore, SQLiteStore
 from tiatoolbox.tools.pyramid import AnnotationTileGenerator, ZoomifyGenerator
 from tiatoolbox.utils.misc import add_from_dat, store_from_dat
+from tiatoolbox.utils.postproc_defs import MultichannelToRGB
 from tiatoolbox.utils.visualization import AnnotationRenderer, colourise_image
 from tiatoolbox.wsicore.wsireader import OpenSlideWSIReader, VirtualWSIReader, WSIReader
 
@@ -166,6 +167,7 @@ def __init__(  # noqa: PLR0915
         self.route("/tileserver/prop_range", methods=["PUT"])(self.prop_range)
         self.route("/tileserver/channels", methods=["GET"])(self.get_channels)
         self.route("/tileserver/channels", methods=["PUT"])(self.set_channels)
+        self.route("/tileserver/enhance", methods=["PUT"])(self.set_enhance)
         self.route("/tileserver/shutdown", methods=["POST"])(self.shutdown)
 
     def _get_session_id(self: TileServer) -> str:
@@ -723,13 +725,32 @@ def prop_range(self: TileServer) -> str:
     def get_channels(self: TileServer) -> Response:
         """Get the channels of the slide."""
         session_id = self._get_session_id()
-        return jsonify(self.layers[session_id]["slide"].post_proc.color_dict)
+        if isinstance(self.layers[session_id]["slide"].post_proc, MultichannelToRGB):
+            return jsonify(
+                {
+                    "channels": self.layers[session_id]["slide"].post_proc.color_dict,
+                    "active": self.layers[session_id]["slide"].post_proc.channels,
+                },
+            )
+        return jsonify({"channels": {}, "active": []})
 
     def set_channels(self: TileServer) -> str:
         """Set the channels of the slide."""
         session_id = self._get_session_id()
-        channels = json.loads(request.form["channels"])
-        self.layers[session_id]["slide"].post_proc.color_dict = channels
+        if isinstance(self.layers[session_id]["slide"].post_proc, MultichannelToRGB):
+            channels = json.loads(request.form["channels"])
+            active = json.loads(request.form["active"])
+            self.layers[session_id]["slide"].post_proc.color_dict = channels
+            self.layers[session_id]["slide"].post_proc.channels = active
+            self.layers[session_id]["slide"].post_proc.is_validated = False
+        return "done"
+
+    def set_enhance(self: TileServer) -> str:
+        """Set the enhance factor of the slide."""
+        session_id = self._get_session_id()
+        enhance = json.loads(request.form["val"])
+        if isinstance(self.layers[session_id]["slide"].post_proc, MultichannelToRGB):
+            self.layers[session_id]["slide"].post_proc.enhance = enhance
         return "done"
 
     @staticmethod

From 6970bae289d5b555d33ca55d70b676109d8774a1 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 22 Aug 2024 20:10:48 +0000
Subject: [PATCH 22/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/test_app_bokeh.py                    | 8 ++++----
 tiatoolbox/visualization/bokeh_app/main.py | 7 +++----
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/tests/test_app_bokeh.py b/tests/test_app_bokeh.py
index e8eec47ec..061930bd9 100644
--- a/tests/test_app_bokeh.py
+++ b/tests/test_app_bokeh.py
@@ -11,19 +11,19 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
+import bokeh.models as bkmodels
 import matplotlib.pyplot as plt
 import numpy as np
 import pytest
 import requests
+from bokeh.application import Application
+from bokeh.application.handlers import FunctionHandler
+from bokeh.events import ButtonClick, DoubleTap, MenuItemClick
 from flask_cors import CORS
 from matplotlib import colormaps
 from PIL import Image
 from scipy.ndimage import label
 
-import bokeh.models as bkmodels
-from bokeh.application import Application
-from bokeh.application.handlers import FunctionHandler
-from bokeh.events import ButtonClick, DoubleTap, MenuItemClick
 from tiatoolbox.data import _fetch_remote_sample
 from tiatoolbox.visualization.bokeh_app import main
 from tiatoolbox.visualization.tileserver import TileServer
diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index f679bbaf1..8f1c1a948 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -14,10 +14,6 @@
 import numpy as np
 import requests
 import torch
-from matplotlib import colormaps
-from PIL import Image
-from requests.adapters import HTTPAdapter, Retry
-
 from bokeh.events import ButtonClick, DoubleTap, MenuItemClick
 from bokeh.io import curdoc
 from bokeh.layouts import column, row
@@ -64,6 +60,9 @@
 from bokeh.models.tiles import WMTSTileSource
 from bokeh.plotting import figure
 from bokeh.util import token
+from matplotlib import colormaps
+from PIL import Image
+from requests.adapters import HTTPAdapter, Retry
 
 # GitHub actions seems unable to find TIAToolbox unless this is here
 sys.path.insert(0, str(Path(__file__).parent.parent.parent.parent))

From 063aba8dd6561d8fdda6af2fb1960019c6b62b07 Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Thu, 22 Aug 2024 22:05:59 +0100
Subject: [PATCH 23/36] fix a test

---
 tiatoolbox/visualization/bokeh_app/main.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index f679bbaf1..2a051e098 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -145,7 +145,7 @@ def get_channel_info() -> dict[str, tuple[int, int, int]]:
     resp = UI["s"].get(f"http://{host2}:5000/tileserver/channels")
     try:
         resp = json.loads(resp.text)
-        return resp["channels"], resp["active"]
+        return resp.get("channels", {}), resp.get("active", [])
     except json.JSONDecodeError:
         return {}, []
 
@@ -272,12 +272,13 @@ def populate_table() -> None:
     source = UI["channel_select"].children[1].children[0].source
     colors, active_channels = get_channel_info()
 
-    new_data = {
-        "channels": list(colors.keys()),
-        "colors": [rgb2hex(color) for color in colors.values()],
-        "active": [channel in active_channels for channel in range(len(colors))],
-    }
-    source.data = new_data
+    if colors is not None:
+        new_data = {
+            "channels": list(colors.keys()),
+            "colors": [rgb2hex(color) for color in colors.values()],
+            "active": [channel in active_channels for channel in range(len(colors))],
+        }
+        source.data = new_data
 
 
 def get_view_bounds(

From 00eb70e8269665b682c29a781b14fc2618b6c551 Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Sun, 25 Aug 2024 16:25:23 +0100
Subject: [PATCH 24/36] more efficient channel select ui

---
 tiatoolbox/visualization/bokeh_app/main.py | 118 +++++++++++++--------
 1 file changed, 71 insertions(+), 47 deletions(-)

diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index da0def679..3d6b3eee0 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -22,7 +22,6 @@
     BoxEditTool,
     Button,
     CheckboxButtonGroup,
-    CheckboxEditor,
     Circle,
     ColorBar,
     ColorPicker,
@@ -159,43 +158,64 @@ def set_channel_info(
     )
 
 
-def create_channel_color_ui() -> Column:
-    """Create the channel select/color management UI."""
-    # Start with an empty ColumnDataSource
-    source = ColumnDataSource(data={"channels": [], "colors": [], "active": []})
+def create_channel_color_ui():
+    channel_source = ColumnDataSource(
+        data={
+            "channels": [],
+            "dummy": [],
+        }
+    )
+    color_source = ColumnDataSource(
+        data={
+            "colors": [],
+            "dummy": [],
+        }
+    )
 
-    # Custom formatter for the color column
     color_formatter = HTMLTemplateFormatter(
-        template="""<div style="background-color: <%= value %>;
-          color: <%= value %>; border: 1px solid #ddd;"><%= value %></div>"""
+        template='<div style="background-color: <%= value %>; color: <%= value %>; border: 1px solid #ddd;"><%= value %></div>'
     )
 
-    columns = [
-        TableColumn(
-            field="channels", title="Channel", editor=StringEditor(), sortable=False
-        ),
-        TableColumn(
-            field="colors",
-            title="Color",
-            editor=StringEditor(),
-            formatter=color_formatter,
-            sortable=False,
-        ),
-        TableColumn(
-            field="active", title="Active", editor=CheckboxEditor(), sortable=False
-        ),
-    ]
-    data_table = DataTable(
-        source=source, columns=columns, editable=True, width=250, height=200
+    channel_table = DataTable(
+        source=channel_source,
+        columns=[
+            TableColumn(
+                field="channels", title="Channel", editor=StringEditor(), sortable=False
+            )
+        ],
+        editable=True,
+        width=200,
+        height=300,
+        selectable="checkbox",
+        autosize_mode="fit_viewport",
+        flow_mode="inline",
+    )
+    color_table = DataTable(
+        source=color_source,
+        columns=[
+            TableColumn(
+                field="colors",
+                title="Color",
+                formatter=color_formatter,
+                editor=StringEditor(),
+                sortable=False,
+            )
+        ],
+        editable=True,
+        width=130,
+        height=300,
+        selectable=True,
+        autosize_mode="none",
+        index_position=None,
+        flow_mode="inline",
     )
 
-    color_picker = ColorPicker(title="Selected Color", width=100)
+    color_picker = ColorPicker(title="Selected Channel Color", width=100)
 
-    def update_selected_color(attr: str, old: str, new: str) -> None:  # noqa: ARG001 # skipcq: PYL-W0613
-        """Channel color picker callback."""
-        selected = source.selected.indices
+    def update_selected_color(attr, old, new):
+        selected = color_source.selected.indices
         if selected:
-            source.patch({"colors": [(selected[0], new)]})
+            color_source.patch({"colors": [(selected[0], new)]})
 
     color_picker.on_change("color", update_selected_color)
 
@@ -205,26 +225,22 @@ def update_selected_color(attr: str, old: str, new: str) -> None:  # noqa: ARG00
 
     def apply_changes() -> None:
         """Apply the changes to the image."""
-        data = source.data
-        colors = dict(zip(data["channels"], data["colors"]))
-        active_channels = [
-            channel for channel, is_active in enumerate(data["active"]) if is_active
-        ]
+        colors = dict(zip(channel_source.data["channels"], color_source.data["colors"]))
+        active_channels = channel_source.selected.indices
 
         set_channel_info({ch: hex2rgb(colors[ch]) for ch in colors}, active_channels)
         change_tiles("slide")
 
     apply_button.on_click(apply_changes)
 
-    def update_color_picker(attr: str, old: str, new: str) -> None:  # noqa: ARG001 # skipcq: PYL-W0613
-        """Update the color picker when a new row is selected."""
+    def update_color_picker(attr, old, new):
         if new:
-            selected_color = source.data["colors"][new[0]]
+            selected_color = color_source.data["colors"][new[0]]
             color_picker.color = selected_color
         else:
             color_picker.color = None
 
-    source.selected.on_change("indices", update_color_picker)
+    color_source.selected.on_change("indices", update_color_picker)
 
     enhance_slider = Slider(
         start=0.1,
@@ -250,10 +266,11 @@ def enhance_cb(attr: str, old: str, new: str) -> None:  # noqa: ARG001 # skipcq:
         text="""
         <p>Instructions:</p>
         <ul>
-            <li>Use the table to view and edit channel properties</li>
-            <li>Click on a row to select a channel</li>
+            <li>Double-click on the 'Active' column to toggle channel visibility</li>
+            <li>Click on a row to select it for color editing</li>
+            <li>Use 'Select All' or 'Deselect All' for quick selection</li>
+            <li>Enable 'Solo Mode' and select a channel to view it alone</li>
             <li>Use the color picker to change the color of the selected channel</li>
-            <li>Check or uncheck the 'Active' column to toggle channel visibility</li>
             <li>Click 'Apply Changes' to update the image</li>
         </ul>
     """
@@ -261,23 +278,30 @@ def enhance_cb(attr: str, old: str, new: str) -> None:  # noqa: ARG001 # skipcq:
 
     return column(
         instructions,
-        column(data_table, row(color_picker, apply_button), enhance_slider),
+        column(
+            row(channel_table, color_table),
+            row(color_picker, apply_button),
+            enhance_slider,
+        ),
     )
 
 
 def populate_table() -> None:
     """Populate the channel color table."""
     # Access the ColumnDataSource from the UI dictionary
-    source = UI["channel_select"].children[1].children[0].source
+    tables = UI["channel_select"].children[1].children[0].children
     colors, active_channels = get_channel_info()
 
     if colors is not None:
-        new_data = {
+        tables[0].source.data = {
             "channels": list(colors.keys()),
+            "dummy": list(colors.keys()),
+        }
+        tables[1].source.data = {
             "colors": [rgb2hex(color) for color in colors.values()],
-            "active": [channel in active_channels for channel in range(len(colors))],
+            "dummy": list(colors.keys()),
         }
-        source.data = new_data
+        tables[0].source.selected.indices = active_channels
 
 
 def get_view_bounds(

From 883ce4036f36055b509656d32bd4221fb624f626 Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Thu, 29 Aug 2024 13:53:24 +0100
Subject: [PATCH 25/36] multichannel ui layout tweak

---
 tiatoolbox/visualization/bokeh_app/main.py | 26 +++++++++++++---------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index 3d6b3eee0..a895a5d2d 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -14,6 +14,10 @@
 import numpy as np
 import requests
 import torch
+from matplotlib import colormaps
+from PIL import Image
+from requests.adapters import HTTPAdapter, Retry
+
 from bokeh.events import ButtonClick, DoubleTap, MenuItemClick
 from bokeh.io import curdoc
 from bokeh.layouts import column, row
@@ -59,9 +63,6 @@
 from bokeh.models.tiles import WMTSTileSource
 from bokeh.plotting import figure
 from bokeh.util import token
-from matplotlib import colormaps
-from PIL import Image
-from requests.adapters import HTTPAdapter, Retry
 
 # GitHub actions seems unable to find TIAToolbox unless this is here
 sys.path.insert(0, str(Path(__file__).parent.parent.parent.parent))
@@ -180,15 +181,19 @@ def create_channel_color_ui():
         source=channel_source,
         columns=[
             TableColumn(
-                field="channels", title="Channel", editor=StringEditor(), sortable=False
+                field="channels",
+                title="Channel",
+                editor=StringEditor(),
+                sortable=False,
+                width=200,
             )
         ],
         editable=True,
         width=200,
-        height=300,
+        height=260,
         selectable="checkbox",
-        autosize_mode="fit_viewport",
-        flow_mode="inline",
+        autosize_mode="none",
+        fit_columns=True,
     )
     color_table = DataTable(
         source=color_source,
@@ -199,18 +204,19 @@ def create_channel_color_ui():
                 formatter=color_formatter,
                 editor=StringEditor(),
                 sortable=False,
+                width=130,
             )
         ],
         editable=True,
         width=130,
-        height=300,
+        height=260,
         selectable=True,
         autosize_mode="none",
         index_position=None,
-        flow_mode="inline",
+        fit_columns=True,
     )
 
-    color_picker = ColorPicker(title="Selected Channel Color", width=100)
+    color_picker = ColorPicker(title="Channel Color", width=100)
 
     def update_selected_color(attr, old, new):
         selected = color_source.selected.indices

From 9df1566355c66b0005cb5541f4ed4fec7e0fd52d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 29 Aug 2024 12:57:12 +0000
Subject: [PATCH 26/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tiatoolbox/visualization/bokeh_app/main.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index a895a5d2d..fbfe1e3cd 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -14,10 +14,6 @@
 import numpy as np
 import requests
 import torch
-from matplotlib import colormaps
-from PIL import Image
-from requests.adapters import HTTPAdapter, Retry
-
 from bokeh.events import ButtonClick, DoubleTap, MenuItemClick
 from bokeh.io import curdoc
 from bokeh.layouts import column, row
@@ -63,6 +59,9 @@
 from bokeh.models.tiles import WMTSTileSource
 from bokeh.plotting import figure
 from bokeh.util import token
+from matplotlib import colormaps
+from PIL import Image
+from requests.adapters import HTTPAdapter, Retry
 
 # GitHub actions seems unable to find TIAToolbox unless this is here
 sys.path.insert(0, str(Path(__file__).parent.parent.parent.parent))

From edd6f63952a8750d3a4fabbf7f8da9988af776de Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Sun, 22 Sep 2024 00:01:51 +0100
Subject: [PATCH 27/36] robustify level sort

---
 tiatoolbox/models/dataset/classification.py | 6 +++++-
 tiatoolbox/wsicore/wsireader.py             | 4 +++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/tiatoolbox/models/dataset/classification.py b/tiatoolbox/models/dataset/classification.py
index cd17dab7e..44a43e318 100644
--- a/tiatoolbox/models/dataset/classification.py
+++ b/tiatoolbox/models/dataset/classification.py
@@ -320,7 +320,11 @@ def __init__(  # skipcq: PY-R1000  # noqa: PLR0915
         elif auto_get_mask and mode == "wsi" and mask_path is None:
             # if no mask provided and `wsi` mode, generate basic tissue
             # mask on the fly
-            mask_reader = self.reader.tissue_mask(resolution=1.25, units="power")
+            try:
+                mask_reader = self.reader.tissue_mask(resolution=1.25, units="power")
+            except:
+                # if power is None, try with mpp
+                mask_reader = self.reader.tissue_mask(resolution=6.0, units="mpp")
             # ? will this mess up  ?
             mask_reader.info = self.reader.info
 
diff --git a/tiatoolbox/wsicore/wsireader.py b/tiatoolbox/wsicore/wsireader.py
index 4e2312aa5..3b5dde262 100644
--- a/tiatoolbox/wsicore/wsireader.py
+++ b/tiatoolbox/wsicore/wsireader.py
@@ -3595,7 +3595,9 @@ def page_area(page: tifffile.TiffPage) -> float:
         self.level_arrays = dict(
             sorted(
                 self.level_arrays.items(),
-                key=lambda x: -np.prod(self._canonical_shape(x[1].array.shape[:2])),
+                key=lambda x: -np.prod(
+                    self._canonical_shape(x[1].array.shape[:2]), dtype=float
+                ),
             )
         )
         # maybe get colors if they exist in metadata

From 3a024dd89a3e8b805a8ac063c043f58f2bd98004 Mon Sep 17 00:00:00 2001
From: behnazelhaminia <behnazelhaminia@yahoo.com>
Date: Thu, 26 Sep 2024 18:49:32 +0100
Subject: [PATCH 28/36] :white_check_mark: Adding  small multiplxed image

---
 tiatoolbox/data/remote_samples.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tiatoolbox/data/remote_samples.yaml b/tiatoolbox/data/remote_samples.yaml
index 5182c87a4..108be3d6b 100644
--- a/tiatoolbox/data/remote_samples.yaml
+++ b/tiatoolbox/data/remote_samples.yaml
@@ -147,3 +147,5 @@ files:
     url: [*modelroot, "predictions/nuclei_mask/nuclick-output.npy"]
   qptiff_sample:
     url: [*wsis, "multiplexed_example.qptiff"]
+  qptiff_sample_small:
+    url: [ *wsis, "multiplexed_example_small.qptiff" ]

From 9d8ac0cdec35ea58ea6350c77d30c7830c6a2617 Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Mon, 4 Nov 2024 14:03:33 +0000
Subject: [PATCH 29/36] dataset fix

---
 tiatoolbox/models/dataset/classification.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tiatoolbox/models/dataset/classification.py b/tiatoolbox/models/dataset/classification.py
index 44a43e318..7180c0265 100644
--- a/tiatoolbox/models/dataset/classification.py
+++ b/tiatoolbox/models/dataset/classification.py
@@ -352,6 +352,8 @@ def __getitem__(self: WSIPatchDataset, idx: int) -> dict:
         """Get an item from the dataset."""
         coords = self.inputs[idx]
         # Read image patch from the whole-slide image
+        if isinstance(self.reader, (Path, str)):
+            self.reader = WSIReader.open(self.reader)
         patch = self.reader.read_bounds(
             coords,
             resolution=self.resolution,

From 41d2fee1d463c3bc728386316b932505e4f98d26 Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Fri, 31 Jan 2025 10:05:35 +0000
Subject: [PATCH 30/36] fix get_channels and address ruff

---
 tiatoolbox/visualization/bokeh_app/main.py | 15 ++++++++++-----
 tiatoolbox/visualization/tileserver.py     |  4 ++++
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index c441624f6..6567eb85f 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -145,7 +145,8 @@ def get_channel_info() -> dict[str, tuple[int, int, int]]:
     try:
         resp = json.loads(resp.text)
         return resp.get("channels", {}), resp.get("active", [])
-    except json.JSONDecodeError:
+    except json.JSONDecodeError as e:
+        logger.warning(f"Error decoding JSON: {e}")
         return {}, []
 
 
@@ -159,7 +160,8 @@ def set_channel_info(
     )
 
 
-def create_channel_color_ui():
+def create_channel_color_ui() -> Column:
+    """Create the multi-channel UI controls."""
     channel_source = ColumnDataSource(
         data={
             "channels": [],
@@ -174,7 +176,8 @@ def create_channel_color_ui():
     )
 
     color_formatter = HTMLTemplateFormatter(
-        template='<div style="background-color: <%= value %>; color: <%= value %>; border: 1px solid #ddd;"><%= value %></div>'
+        template="""<div style='background-color: <%= value %>; color:
+          <%= value %>; border: 1px solid #ddd;'><%= value %></div>"""
     )
 
     channel_table = DataTable(
@@ -218,7 +221,8 @@ def create_channel_color_ui():
 
     color_picker = ColorPicker(title="Channel Color", width=100)
 
-    def update_selected_color(attr, old, new):
+    def update_selected_color(attr: str, old: str, new: str) -> None:  # noqa: ARG001
+        """Update the selected color in multichannel ui."""
         selected = color_source.selected.indices
         if selected:
             color_source.patch({"colors": [(selected[0], new)]})
@@ -239,7 +243,8 @@ def apply_changes() -> None:
 
     apply_button.on_click(apply_changes)
 
-    def update_color_picker(attr, old, new):
+    def update_color_picker(attr: str, old: str, new: str) -> None:  # noqa: ARG001
+        """Update the color picker when a new channel is selected."""
         if new:
             selected_color = color_source.data["colors"][new[0]]
             color_picker.color = selected_color
diff --git a/tiatoolbox/visualization/tileserver.py b/tiatoolbox/visualization/tileserver.py
index 5b637e169..26b480643 100644
--- a/tiatoolbox/visualization/tileserver.py
+++ b/tiatoolbox/visualization/tileserver.py
@@ -726,6 +726,10 @@ def get_channels(self: TileServer) -> Response:
         """Get the channels of the slide."""
         session_id = self._get_session_id()
         if isinstance(self.layers[session_id]["slide"].post_proc, MultichannelToRGB):
+            if self.layers[session_id]["slide"].post_proc.color_dict is None:
+                _ = self.layers[session_id]["slide"].slide_thumbnail(
+                    resolution=8.0, units="mpp"
+                )
             return jsonify(
                 {
                     "channels": self.layers[session_id]["slide"].post_proc.color_dict,

From 04259174a9e34a04d6e0e41338c84454ddda1fcc Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Fri, 31 Jan 2025 13:26:49 +0000
Subject: [PATCH 31/36] precommit fixes

---
 tiatoolbox/models/dataset/classification.py |  2 +-
 tiatoolbox/visualization/bokeh_app/main.py  | 22 +++++++++++++++------
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/tiatoolbox/models/dataset/classification.py b/tiatoolbox/models/dataset/classification.py
index 7180c0265..4881dc344 100644
--- a/tiatoolbox/models/dataset/classification.py
+++ b/tiatoolbox/models/dataset/classification.py
@@ -322,7 +322,7 @@ def __init__(  # skipcq: PY-R1000  # noqa: PLR0915
             # mask on the fly
             try:
                 mask_reader = self.reader.tissue_mask(resolution=1.25, units="power")
-            except:
+            except ValueError:
                 # if power is None, try with mpp
                 mask_reader = self.reader.tissue_mask(resolution=6.0, units="mpp")
             # ? will this mess up  ?
diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index 6567eb85f..2c20bcc02 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -146,7 +146,7 @@ def get_channel_info() -> dict[str, tuple[int, int, int]]:
         resp = json.loads(resp.text)
         return resp.get("channels", {}), resp.get("active", [])
     except json.JSONDecodeError as e:
-        logger.warning(f"Error decoding JSON: {e}")
+        logger.warning("Error decoding JSON: %s", e)
         return {}, []
 
 
@@ -221,7 +221,11 @@ def create_channel_color_ui() -> Column:
 
     color_picker = ColorPicker(title="Channel Color", width=100)
 
-    def update_selected_color(attr: str, old: str, new: str) -> None:  # noqa: ARG001
+    def update_selected_color( # noqa: ARG001 # skipcq: PYL-W0613
+            attr: str, 
+            old: str, 
+            new: str
+            ) -> None:
         """Update the selected color in multichannel ui."""
         selected = color_source.selected.indices
         if selected:
@@ -243,7 +247,10 @@ def apply_changes() -> None:
 
     apply_button.on_click(apply_changes)
 
-    def update_color_picker(attr: str, old: str, new: str) -> None:  # noqa: ARG001
+    def update_color_picker(  # noqa: ARG001 # skipcq: PYL-W0613
+            attr: str, 
+            old: str, 
+            new: str) -> None:
         """Update the color picker when a new channel is selected."""
         if new:
             selected_color = color_source.data["colors"][new[0]]
@@ -262,7 +269,10 @@ def update_color_picker(attr: str, old: str, new: str) -> None:  # noqa: ARG001
         width=200,
     )
 
-    def enhance_cb(attr: str, old: str, new: str) -> None:  # noqa: ARG001 # skipcq: PYL-W0613
+    def enhance_cb(  # noqa: ARG001 # skipcq: PYL-W0613
+            attr: str, 
+            old: str, 
+            new: str) -> None:
         """Enhance slider callback."""
         UI["s"].put(
             f"http://{host2}:5000/tileserver/enhance",
@@ -929,14 +939,14 @@ def populate_slide_list(slide_folder: Path, search_txt: str | None = None) -> No
     UI["slide_select"].options = file_list
 
 
-def filter_input_cb(attr: str, old: str, new: str) -> None:  # noqa: ARG001
+def filter_input_cb(attr: str, old: str, new: str) -> None:  # noqa: ARG001 # skipcq: PYL-W0613
     """Change predicate to be used to filter annotations."""
     build_predicate()
     UI["vstate"].update_state = 1
     UI["vstate"].to_update.update(["overlay"])
 
 
-def cprop_input_cb(attr: str, old: str, new: list[str]) -> None:  # noqa: ARG001
+def cprop_input_cb(attr: str, old: str, new: list[str]) -> None:  # noqa: ARG001 # skipcq: PYL-W0613
     """Change property to color by."""
     if len(new) == 0:
         return

From e4b44d75c2a35f9497b1952655cc7926fefabeca Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Fri, 31 Jan 2025 14:04:18 +0000
Subject: [PATCH 32/36] dont fix arg001

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2d29ca7c8..f807b6593 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -105,7 +105,7 @@ lint.select = [
   "ASYNC", # flake8-async
 ]
 # Ignore rules which conflict with ruff formatter.
-lint.ignore = ["COM812", "ISC001",]
+lint.ignore = ["COM812", "ISC001", "RUF100"]
 # Allow Ruff to discover `*.ipynb` files.
 include = ["*.py", "*.pyi", "**/pyproject.toml", "*.ipynb"]
 

From 4ca6660f7027d060831780e830aa0eba3668bcbe Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 31 Jan 2025 14:05:12 +0000
Subject: [PATCH 33/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tiatoolbox/visualization/bokeh_app/main.py | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index 2c20bcc02..8feb9d13a 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -221,11 +221,9 @@ def create_channel_color_ui() -> Column:
 
     color_picker = ColorPicker(title="Channel Color", width=100)
 
-    def update_selected_color( # noqa: ARG001 # skipcq: PYL-W0613
-            attr: str, 
-            old: str, 
-            new: str
-            ) -> None:
+    def update_selected_color(  # noqa: ARG001 # skipcq: PYL-W0613
+        attr: str, old: str, new: str
+    ) -> None:
         """Update the selected color in multichannel ui."""
         selected = color_source.selected.indices
         if selected:
@@ -248,9 +246,8 @@ def apply_changes() -> None:
     apply_button.on_click(apply_changes)
 
     def update_color_picker(  # noqa: ARG001 # skipcq: PYL-W0613
-            attr: str, 
-            old: str, 
-            new: str) -> None:
+        attr: str, old: str, new: str
+    ) -> None:
         """Update the color picker when a new channel is selected."""
         if new:
             selected_color = color_source.data["colors"][new[0]]
@@ -270,9 +267,8 @@ def update_color_picker(  # noqa: ARG001 # skipcq: PYL-W0613
     )
 
     def enhance_cb(  # noqa: ARG001 # skipcq: PYL-W0613
-            attr: str, 
-            old: str, 
-            new: str) -> None:
+        attr: str, old: str, new: str
+    ) -> None:
         """Enhance slider callback."""
         UI["s"].put(
             f"http://{host2}:5000/tileserver/enhance",

From 312e5b502b540296a94c2eea3b9d69644534548d Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Fri, 31 Jan 2025 14:18:07 +0000
Subject: [PATCH 34/36] precommit..

---
 tiatoolbox/visualization/bokeh_app/main.py | 30 ++++++++++++++++------
 1 file changed, 22 insertions(+), 8 deletions(-)

diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index 8feb9d13a..dc3af9314 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -221,8 +221,10 @@ def create_channel_color_ui() -> Column:
 
     color_picker = ColorPicker(title="Channel Color", width=100)
 
-    def update_selected_color(  # noqa: ARG001 # skipcq: PYL-W0613
-        attr: str, old: str, new: str
+    def update_selected_color(
+        attr: str,  # noqa: ARG001 # skipcq: PYL-W0613
+        old: str,  # noqa: ARG001 # skipcq: PYL-W0613
+        new: str,
     ) -> None:
         """Update the selected color in multichannel ui."""
         selected = color_source.selected.indices
@@ -245,8 +247,10 @@ def apply_changes() -> None:
 
     apply_button.on_click(apply_changes)
 
-    def update_color_picker(  # noqa: ARG001 # skipcq: PYL-W0613
-        attr: str, old: str, new: str
+    def update_color_picker(
+        attr: str,  # noqa: ARG001 # skipcq: PYL-W0613
+        old: str,  # noqa: ARG001 # skipcq: PYL-W0613
+        new: str,
     ) -> None:
         """Update the color picker when a new channel is selected."""
         if new:
@@ -266,8 +270,10 @@ def update_color_picker(  # noqa: ARG001 # skipcq: PYL-W0613
         width=200,
     )
 
-    def enhance_cb(  # noqa: ARG001 # skipcq: PYL-W0613
-        attr: str, old: str, new: str
+    def enhance_cb(
+        attr: str,  # noqa: ARG001 # skipcq: PYL-W0613
+        old: str,  # noqa: ARG001 # skipcq: PYL-W0613
+        new: str,
     ) -> None:
         """Enhance slider callback."""
         UI["s"].put(
@@ -935,14 +941,22 @@ def populate_slide_list(slide_folder: Path, search_txt: str | None = None) -> No
     UI["slide_select"].options = file_list
 
 
-def filter_input_cb(attr: str, old: str, new: str) -> None:  # noqa: ARG001 # skipcq: PYL-W0613
+def filter_input_cb(
+    attr: str,  # noqa: ARG001 # skipcq: PYL-W0613
+    old: str,  # noqa: ARG001 # skipcq: PYL-W0613
+    new: str,  # noqa: ARG001 # skipcq: PYL-W0613
+) -> None:
     """Change predicate to be used to filter annotations."""
     build_predicate()
     UI["vstate"].update_state = 1
     UI["vstate"].to_update.update(["overlay"])
 
 
-def cprop_input_cb(attr: str, old: str, new: list[str]) -> None:  # noqa: ARG001 # skipcq: PYL-W0613
+def cprop_input_cb(
+    attr: str,  # noqa: ARG001 # skipcq: PYL-W0613
+    old: str,  # noqa: ARG001 # skipcq: PYL-W0613
+    new: list[str],
+) -> None:
     """Change property to color by."""
     if len(new) == 0:
         return

From 68c375cd7ddafe48abb09a4de2b224cf1dacd90e Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Fri, 14 Feb 2025 05:43:22 +0000
Subject: [PATCH 35/36] comet format support

---
 tiatoolbox/utils/postproc_defs.py | 10 +++++++---
 tiatoolbox/wsicore/wsireader.py   | 10 ++++++++--
 2 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/tiatoolbox/utils/postproc_defs.py b/tiatoolbox/utils/postproc_defs.py
index a0954384c..54ca54ccc 100644
--- a/tiatoolbox/utils/postproc_defs.py
+++ b/tiatoolbox/utils/postproc_defs.py
@@ -4,6 +4,7 @@
 
 import colorsys
 import warnings
+from typing import Any
 
 import numpy as np
 
@@ -13,7 +14,7 @@ class MultichannelToRGB:
 
     def __init__(
         self: MultichannelToRGB,
-        color_dict: list[tuple[float, float, float]] | None = None,
+        color_dict: dict[str : tuple[float, float, float]] | None = None,
     ) -> None:
         """Initialize the MultichannelToRGB converter.
 
@@ -60,7 +61,7 @@ def validate(self: MultichannelToRGB, n: int) -> None:
         msg = f"Number of colors: {n_colors} does not match channels in image: {n}."
         raise ValueError(msg)
 
-    def generate_colors(self: MultichannelToRGB, n_channels: int) -> np.ndarray:
+    def generate_colors(self: MultichannelToRGB, n_channels: int) -> None:
         """Generate a set of visually distinct colors.
 
         Args:
@@ -97,6 +98,9 @@ def __call__(self: MultichannelToRGB, image: np.ndarray) -> np.ndarray:
         if not self.is_validated:
             self.validate(n)
 
+        if image.dtype == np.uint16:
+            image = (image / 256).astype(np.uint8)
+
         # Convert to RGB image
         rgb_image = (
             np.einsum(
@@ -111,7 +115,7 @@ def __call__(self: MultichannelToRGB, image: np.ndarray) -> np.ndarray:
         # Clip  to ensure in valid range and return
         return np.clip(rgb_image, 0, 255).astype(np.uint8)
 
-    def __setattr__(self: MultichannelToRGB, name: str, value: np.Any) -> None:
+    def __setattr__(self: MultichannelToRGB, name: str, value: Any) -> None:
         """Ensure that colors is updated if color_dict is updated."""
         if name == "color_dict" and value is not None:
             self.colors = np.array(list(value.values()), dtype=np.float32)
diff --git a/tiatoolbox/wsicore/wsireader.py b/tiatoolbox/wsicore/wsireader.py
index d52634707..f3c2de13e 100644
--- a/tiatoolbox/wsicore/wsireader.py
+++ b/tiatoolbox/wsicore/wsireader.py
@@ -409,9 +409,12 @@ def open(  # noqa: PLR0911
             return TIFFWSIReader(input_path, mpp=mpp, power=power, post_proc=post_proc)
 
         if last_suffix in (".tif", ".tiff"):
-            tiff_wsi = _handle_tiff_wsi(
+            tiff_wsi = TIFFWSIReader(
                 input_path, mpp=mpp, power=power, post_proc=post_proc
             )
+            # tiff_wsi = _handle_tiff_wsi(
+            #    input_path, mpp=mpp, power=power, post_proc=post_proc
+            # )
             if tiff_wsi is not None:
                 return tiff_wsi
 
@@ -3792,8 +3795,11 @@ def _get_ome_objective_power(
             return None
 
         objective_settings = xml_series.find("ome:ObjectiveSettings", namespaces)
+        if objective_settings is None:
+            # try alternative tag
+            objective_settings = xml_series.find("ome:Objective", namespaces)
         instrument_ref_id = instrument_ref.attrib["ID"]
-        objective_settings_id = objective_settings.attrib["ID"]
+        objective_settings_id = "Objective:0"  # objective_settings.attrib["ID"]
         instruments = {
             instrument.attrib["ID"]: instrument
             for instrument in xml.findall("ome:Instrument", namespaces)

From b228d78ce41db7e13bee269c7580a83ad2930988 Mon Sep 17 00:00:00 2001
From: measty <20169086+measty@users.noreply.github.com>
Date: Fri, 14 Mar 2025 17:18:11 +0000
Subject: [PATCH 36/36] metadata update

---
 tiatoolbox/wsicore/wsireader.py | 60 +++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/tiatoolbox/wsicore/wsireader.py b/tiatoolbox/wsicore/wsireader.py
index f3c2de13e..ecd4a3357 100644
--- a/tiatoolbox/wsicore/wsireader.py
+++ b/tiatoolbox/wsicore/wsireader.py
@@ -412,6 +412,8 @@ def open(  # noqa: PLR0911
             tiff_wsi = TIFFWSIReader(
                 input_path, mpp=mpp, power=power, post_proc=post_proc
             )
+            # temporary force to use TIFFWSIReader for tiffs as openslide doesnt work with comet
+            # remove before merging
             # tiff_wsi = _handle_tiff_wsi(
             #    input_path, mpp=mpp, power=power, post_proc=post_proc
             # )
@@ -3633,6 +3635,64 @@ def _get_colors_from_meta(self: TIFFWSIReader) -> None:
                     else:
                         color_dict[key] = mcolors.to_rgb(value)
                 self.post_proc.color_dict = color_dict
+                return
+
+            # try alternate metadata format
+            # Build a map from filter pair string -> color label or RGB string
+            # from the <FilterColors> section
+            filter_colors = {}
+            filter_colors_section = root.find(".//FilterColors")
+            if filter_colors_section is not None:
+                keys = filter_colors_section.findall(".//FilterColors-k")
+                vals = filter_colors_section.findall(".//FilterColors-v")
+                for k, v in zip(keys, vals):
+                    filter_colors[k.text] = v.text
+
+            # Helper function to convert color strings like "Lime" or "255, 128, 0" into (R,G,B)
+            def color_string_to_rgb(s):
+                if "," in s:
+                    return tuple(int(x.strip()) / 255 for x in s.split(","))
+                return mcolors.to_rgb(s)
+
+            # 2) For each <ScanBands-i>, find the channel's name and figure out
+            #    which filter pair it uses, then match that to a color.
+            channel_dict = {}
+
+            for scan_band in root.findall(".//ScanBands-i"):
+                # Inside a <ScanBands-i> there is a <Bands-i> with a <Name> tag
+                bands_i = scan_band.find(".//Bands-i")
+                if bands_i is not None:
+                    band_name_element = bands_i.find("Name")
+                    if band_name_element is not None:
+                        channel_name = band_name_element.text.strip()
+
+                        # Grab the filter pair manufacturer info
+                        filter_pair = scan_band.find(".//FilterPair")
+                        if filter_pair is not None:
+                            emission_part = filter_pair.find(
+                                ".//EmissionFilter/FixedFilter/PartNumber"
+                            )
+                            excitation_part = filter_pair.find(
+                                ".//ExcitationFilter/FixedFilter/PartNumber"
+                            )
+                            if (
+                                emission_part is not None
+                                and excitation_part is not None
+                            ):
+                                matching_rgb = (1.0, 1.0, 1.0)  # default white
+                                for fc_key, fc_val in filter_colors.items():
+                                    # if both part numbers appear in the FilterColors-k string, assume it's the match
+                                    if (
+                                        emission_part.text in fc_key
+                                        and excitation_part.text in fc_key
+                                    ):
+                                        matching_rgb = color_string_to_rgb(fc_val)
+                                        break
+
+                                channel_dict[channel_name] = matching_rgb
+
+            if len(channel_dict) > 0:
+                self.post_proc.color_dict = channel_dict
 
     def _canonical_shape(self: TIFFWSIReader, shape: IntPair) -> tuple:
         """Make a level shape tuple in YXS order.