From 230ba66606b72d52805c072929a20f9498b6f551 Mon Sep 17 00:00:00 2001 From: toloudis Date: Tue, 26 May 2026 19:06:38 -0700 Subject: [PATCH 1/2] brand updates --- CMake/conf.py.cmake | 4 ++-- CMakeLists.txt | 4 ++-- CONTRIBUTING.md | 4 ++-- HELP.txt | 2 +- agave_app/aboutDialog.cpp | 14 +++++++------- agave_app/citationDialog.cpp | 4 ++-- agave_app/main.cpp | 2 +- agave_app/version.rc | 2 +- agave_pyclient/agave_pyclient/__init__.py | 2 +- docs/agave.rst | 4 ++-- docs/conf.py | 4 ++-- 11 files changed, 23 insertions(+), 23 deletions(-) diff --git a/CMake/conf.py.cmake b/CMake/conf.py.cmake index dea60156e..0d6b7860d 100644 --- a/CMake/conf.py.cmake +++ b/CMake/conf.py.cmake @@ -18,8 +18,8 @@ # -- Project information ----------------------------------------------------- project = "AGAVE" -copyright = "2020, Allen Institute for Cell Science" -author = "Allen Institute for Cell Science" +copyright = "2020-26, Allen Institute" +author = "Allen Institute" # The full version, including alpha/beta/rc tags release = "@PROJECT_VERSION@" diff --git a/CMakeLists.txt b/CMakeLists.txt index 2debcb35d..f29d77f6e 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -148,7 +148,7 @@ CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/CMake/conf.py.cmake ${CMAKE_SOURCE_DIR}/docs/ # ##################### find_package(Qt6QTiffPlugin 6.9.3 REQUIRED PATHS ${Qt6Gui_DIR}) -set(CPACK_PACKAGE_VENDOR "Allen Institute for Cell Science") +set(CPACK_PACKAGE_VENDOR "Allen Institute") set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "AGAVE is a viewer for 4D multichannel microscopy images, using physically based lighting and rendering.") set(CPACK_PACKAGE_NAME "AGAVE") @@ -388,7 +388,7 @@ else() # Linux ) set(CPACK_GENERATOR "DEB") set(CPACK_DEBIAN_PACKAGE_NAME "agave") - set(CPACK_PACKAGE_CONTACT "Allen Institute for Cell Science") + set(CPACK_PACKAGE_CONTACT "Allen Institute") include(CPack) endif(WIN32) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 366e578cf..4185a1b79 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,6 +1,6 @@ -# Contributing to Allen Institute for Cell Science Open Source +# Contributing to Allen Institute Open Source -Thank you for your interest in contributing to this Allen Institute for Cell Science open source project! This document is +Thank you for your interest in contributing to this Allen Institute open source project! This document is a set of guidelines to help you contribute to this project. ## Code of Conduct diff --git a/HELP.txt b/HELP.txt index 077bf57d1..b873d786e 100644 --- a/HELP.txt +++ b/HELP.txt @@ -8,7 +8,7 @@ The volume viewer is designed and optimized for display of multi-channel 16-bit 2. Unzip the zip file and run the AGAVE app. A GUI window will open. If initialization fails for some reason, a logfile.log file will be produced in the same directory as the app. 3. File-->Open volume... The viewer currently only supports .tif or .czi files containing z-stack data. Currently only 16-bit unsigned pixels are supported. -The volume data must fit in GPU memory uncompressed, so please try loading no more than a few GB. Files containing time sequences will only load the first time sample. The test data set for the development of this viewer was the data set of the Allen Institute for Cell Science. Images from that data set are found at https://www.allencell.org/3d-cell-viewer.html and https://www.allencell.org/cell-feature-explorer.html where you can load a cell into the 3D viewer in your browser and click the Download button to get the full resolution OME TIFF file. Those images should load correctly into this viewer. +The volume data must fit in GPU memory uncompressed, so please try loading no more than a few GB. Files containing time sequences will only load the first time sample. The test data set for the development of this viewer was data from Cell Science at the Allen Institute. Images from that data set are found at https://www.allencell.org/3d-cell-viewer.html and https://www.allencell.org/cell-feature-explorer.html where you can load a cell into the 3D viewer in your browser and click the Download button to get the full resolution OME TIFF file. Those images should load correctly into this viewer. 4. Initially, it is likely that your volume data will appear as a solid brick. The Appearance panel is the one to focus on first. Note that you can "tear away" the tab to place it anywhere on your desktop and resize it. (Drag and drop from the "Appearance" title area.) diff --git a/agave_app/aboutDialog.cpp b/agave_app/aboutDialog.cpp index fe08928b3..6e186ce3e 100644 --- a/agave_app/aboutDialog.cpp +++ b/agave_app/aboutDialog.cpp @@ -37,13 +37,13 @@ AboutDialog::AboutDialog() layout->addWidget(text); label = new QLabel(this); - label->setText( - "AGAVE is made possible through the hard work and dedication of engineers, designers, and scientists at the Allen " - "Institute for Cell Science and through the continued philanthropy of the Paul Allen estate." - "
" - "
" - "Copyright 2023 The Allen Institute. All rights reserved.
" - ""); + label->setText("AGAVE is made possible through the hard work and dedication of engineers, designers, and scientists " + "in Cell Science at the Allen " + "Institute and through the continued philanthropy of the Paul Allen estate." + "
" + "
" + "Copyright 2023-26 The Allen Institute. All rights reserved.
" + ""); label->setWordWrap(true); layout->addWidget(label); diff --git a/agave_app/citationDialog.cpp b/agave_app/citationDialog.cpp index ac85af115..060621399 100644 --- a/agave_app/citationDialog.cpp +++ b/agave_app/citationDialog.cpp @@ -25,7 +25,7 @@ CitationDialog::CitationDialog() auto citationtext = new QLabel(this); citationtext->setText("Daniel Toloudis, AGAVE Contributors (" + syear + "). AGAVE: Advanced GPU Accelerated Volume Explorer (Version " + qApp->applicationVersion() + - ") [Computer software]. Allen Institute for Cell Science. "); citationtext->setFrameShape(QFrame::Panel); @@ -52,7 +52,7 @@ CitationDialog::CitationDialog() "  url = {" + agaveUrl + "},
" - "  organization = {Allen Institute for Cell Science},
" + "  organization = {Allen Institute, Cell Science},
" "  note = {Computer Software}
" "}
"); citationtext2->setFrameShape(QFrame::Panel); diff --git a/agave_app/main.cpp b/agave_app/main.cpp index 5a4d4f674..5e1b7b6d1 100644 --- a/agave_app/main.cpp +++ b/agave_app/main.cpp @@ -176,7 +176,7 @@ main(int argc, char* argv[]) QApplication::setAttribute(Qt::AA_EnableHighDpiScaling); QApplication::setStyle("fusion"); AgaveApplication a(argc, argv); - AgaveApplication::setOrganizationName("Allen Institute for Cell Science"); + AgaveApplication::setOrganizationName("Allen Institute"); AgaveApplication::setOrganizationDomain("allencell.org"); AgaveApplication::setApplicationName("AGAVE"); AgaveApplication::setApplicationVersion(AICS_VERSION_STRING); diff --git a/agave_app/version.rc b/agave_app/version.rc index dce7d44ef..e6a536716 100644 --- a/agave_app/version.rc +++ b/agave_app/version.rc @@ -18,7 +18,7 @@ BEGIN BEGIN BLOCK "040904E4" BEGIN - VALUE "CompanyName", "Allen Institute for Cell Science" + VALUE "CompanyName", "Allen Institute" VALUE "FileVersion", AICS_VERSION_STRING VALUE "ProductName", "AGAVE" VALUE "ProductVersion", AICS_VERSION_STRING diff --git a/agave_pyclient/agave_pyclient/__init__.py b/agave_pyclient/agave_pyclient/__init__.py index 13a9417f3..cc2856d2b 100644 --- a/agave_pyclient/agave_pyclient/__init__.py +++ b/agave_pyclient/agave_pyclient/__init__.py @@ -4,7 +4,7 @@ from .agave import AgaveRenderer # noqa: F401 -__author__ = "Daniel Toloudis, Allen Institute for Cell Science" +__author__ = "Daniel Toloudis, Allen Institute" __email__ = "danielt@alleninstitute.org" # Do not edit this string manually, always use bumpversion # Details in CONTRIBUTING.md diff --git a/docs/agave.rst b/docs/agave.rst index 8b475fbb2..71bebe95d 100644 --- a/docs/agave.rst +++ b/docs/agave.rst @@ -744,7 +744,7 @@ Citation .. |year| date:: %Y -Daniel Toloudis, AGAVE Contributors (|year|). AGAVE: Advanced GPU Accelerated Volume Explorer (Version |release|) [Computer software]. Allen Institute for Cell Science. https://github.com/allen-cell-animated/agave +Daniel Toloudis, AGAVE Contributors (|year|). AGAVE: Advanced GPU Accelerated Volume Explorer (Version |release|) [Computer software]. Allen Institute, Cell Science. https://github.com/allen-cell-animated/agave bibtex: @@ -756,7 +756,7 @@ bibtex: year = {|year|}, version = {|release|}, url = {https://github.com/allen-cell-animated/agave}, - organization = {Allen Institute for Cell Science}, + organization = {Allen Institute, Cell Science}, note = {Computer Software} } diff --git a/docs/conf.py b/docs/conf.py index 3feec93df..dc57654bd 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -18,8 +18,8 @@ # -- Project information ----------------------------------------------------- project = "AGAVE" -copyright = "2020, Allen Institute for Cell Science" -author = "Allen Institute for Cell Science" +copyright = "2020-26, Allen Institute" +author = "Allen Institute" # The full version, including alpha/beta/rc tags release = "1.9.0" From a74dd130008b09987708653e44d27f1321533b42 Mon Sep 17 00:00:00 2001 From: Lyndsay <93954795+lynwilhelm@users.noreply.github.com> Date: Wed, 27 May 2026 14:02:00 -0700 Subject: [PATCH 2/2] Apply suggestion from @lynwilhelm --- agave_app/aboutDialog.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/agave_app/aboutDialog.cpp b/agave_app/aboutDialog.cpp index 6e186ce3e..6bf8e33c6 100644 --- a/agave_app/aboutDialog.cpp +++ b/agave_app/aboutDialog.cpp @@ -38,7 +38,7 @@ AboutDialog::AboutDialog() label = new QLabel(this); label->setText("AGAVE is made possible through the hard work and dedication of engineers, designers, and scientists " - "in Cell Science at the Allen " + "in the cell science accelerator at the Allen " "Institute and through the continued philanthropy of the Paul Allen estate." "
" "
"