Tifffile support in WSIReader #3278
Merged
Conversation
This file contains hidden or 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
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Member
Author
|
@Nic-Ma could you please take a look at this and run |
Contributor
|
/build |
Nic-Ma
reviewed
Nov 8, 2021
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Nic-Ma
approved these changes
Nov 11, 2021
Contributor
Nic-Ma
left a comment
Nic-Ma
left a comment
There was a problem hiding this comment.
Looks good to me.
Thanks for the update.
Contributor
|
/build |
1 similar comment
Contributor
|
/build |
Contributor
|
/build |
1 similar comment
Contributor
|
/build |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
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Outdated suggestions cannot be applied.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.
Fixes #3251
Description
This PR adds support for
tifffilein WSIReader to read TIFF files (which is common in histopathology whole slide imaging). Whilecucimandopenslideboth can load patches from large whole slide images without loading the entire image into memory,tifffileloads the entire image into before extracting any patch. Thus memory consideration is needed when usingtifffilefor patch extraction.Status
Ready
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.