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175v2 add consep segmentation dataset #544

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wants to merge 31 commits into from
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175v2 add consep segmentation dataset #544

wants to merge 31 commits into from

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roman807
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@roman807 roman807 commented Jun 24, 2024 •
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closes #175

(#517 should be merged first)

ioangatop and others added 28 commits April 30, 2024 09:34
@ioangatop
Add simple decoder networks for segmentation tasks (#404)
2b5a1ce
@ioangatop
Add timm encoder networks (#403)
a7e65e5
@ioangatop
Add SemanticSegmentation module (#410)
ad392e8
@ioangatop
Add TotalSegmentator2D segmentation downstream task (#413)
4ef3afb
@ioangatop
Add dice score in TotalSegmentator2D task (#423)
07fbd08
@ioangatop
Allow to use subclasses in TotalSegmentator2D (#435)
a6fd246
@ioangatop
Create a callback to visualise the segmentation results (#424)
db5a578
@ioangatop
Improve the mask loading in TotalSegmentator2D (#440)
7656ae6
@ioangatop
Add per class metrics dice score in TotalSegmentator2D (#447)
702f634
@ioangatop
Support int16 training on TotalSegementator2D (#443)
434cacb
@ioangatop
Normalisations and transforms for int16 image types (#457)
35bb532
@ioangatop
Fix default segmentation metrics (#503)
c43b8ad
@ioangatop
Add support for multi-level embeddings training in segmentation tasks (…
b009aec 
…#501)
@ioangatop
merge with main
19c92cd
@ioangatop
update with main
cf54cad
@ioangatop
Add dataset licence and env var for dataset download (#516)
cfa47c9
@ioangatop
Merge branch 'main' into 402-aggregated-feature-segmentation-downstre…
cc23d6a 
…am-evaluation-tasks
@ioangatop
Minor updates on semantic segmentation tasks (#519)
6fefade
@ioangatop
Fix SemanticSegmentationLogger callback write frequency (#521)
3b326a0
@ioangatop
Add ModelCheckpoint and EarlyStopping in TotalSegmentator2D` task (…
fb948a0 
…#523)
@ioangatop
Minor fixes in SemanticSegmentationModule (#525)
4ac910e
@ioangatop
Support the full TotalSegmentator2D dataset (#535)
6a00235
@ioangatop
Merge branch 'main' into 402-aggregated-feature-segmentation-downstre…
85a4aba 
…am-evaluation-tasks
@ioangatop
Add test dataloader in TotalSegmentator2D
3d523ca
@roman807
added consep
5f3f2dc
@roman807
updated io
9515eae
@roman807
merge main
007fc68
@roman807
merge main
5b3bc23
@roman807 roman807 linked an issue Jun 24, 2024 that may be closed by this pull request
Add CoNSeP segmentation Dataset #175
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@nkaenzig nkaenzig changed the base branch from main to 402-aggregated-feature-segmentation-downstream-evaluation-tasks June 25, 2024 06:44
@nkaenzig nkaenzig changed the base branch from 402-aggregated-feature-segmentation-downstream-evaluation-tasks to main June 25, 2024 06:45
nkaenzig
nkaenzig reviewed Jun 25, 2024
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Looks good, left some minor comments.
As discussed offline, I'll look into a version of this that does patching.

src/eva/vision/data/datasets/segmentation/consep.py Outdated Show resolved Hide resolved
src/eva/vision/data/datasets/segmentation/consep.py Outdated Show resolved Hide resolved
src/eva/vision/data/datasets/segmentation/consep.py Outdated Show resolved Hide resolved
src/eva/vision/data/datasets/segmentation/consep.py Outdated Show resolved Hide resolved
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will be covered here: #547

@roman807 roman807 closed this Jun 26, 2024
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Add CoNSeP segmentation Dataset
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@roman807 @nkaenzig @ioangatop