✨ Add on-the-fly Registered Slide Visualization #875
+728
−4
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…toolbox into add-registered-slide-vis
for more information, see https://pre-commit.ci
shaneahmed
changed the title
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #875 +/- ##
===========================================
- Coverage 99.90% 98.42% -1.49%
===========================================
Files 70 70
Lines 8735 8885 +150
Branches 1149 1164 +15
===========================================
+ Hits 8727 8745 +18
- Misses 3 133 +130
- Partials 5 7 +2 ☔ View full report in Codecov by Sentry. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR is a rough draft of code to allow a registration transform to be loaded as an 'overlay', which will allow the slide to be viewed as if that registration transform had been applied to it. This will work with either an affine transformation saved as a .npy, or a non-rigid one represented by a SimpleITK displacement field saved as a .mha (such as what would be output by DeeperHistoReg, for example).
It introduces a new WSIReader subclass called TransformedWSIReader, which when initialized with a slide and transformation will apply the transformation on the fly when regions are requested.
It also adds '.npy' and '.mha' to the overlay types the visualization tool picks up; upon loading one of these types, the current slide will be opened as a TransformedWSIReader with that transform, allowing it to be visualized on the fly as a registered slide.
still to do: