Ecosyste.ms: Issues

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GitHub / mahmoodlab/CLAM issues and pull requests

#274 - Eval script usage

Issue - State: open - Opened by rohith2011 about 1 month ago

#273 - Earlyfusion

Pull Request - State: closed - Opened by rzuberi about 1 month ago

#272 - Can't install CLAM through env.yml file

Issue - State: closed - Opened by mguzm4n about 2 months ago - 1 comment

#271 - ViT？

Issue - State: open - Opened by sjjadsa about 2 months ago

#270 - some questions about parameter setting of clustering in main.py

Issue - State: closed - Opened by GeneGee about 2 months ago

#268 - Error while executing main.py

Issue - State: closed - Opened by JTatsuya 2 months ago - 2 comments

#267 - Update eval.py

Pull Request - State: open - Opened by lucyOCg 3 months ago

#266 - The time that CONCH takes

Issue - State: closed - Opened by TXPsim 3 months ago - 2 comments

#265 - Heatmaps visualization

Issue - State: closed - Opened by BioCoderR 3 months ago - 1 comment

#264 - Identify tumor regions

Issue - State: closed - Opened by wangzhengxiao 3 months ago - 1 comment
Labels: scientific discussion

#263 - model types 'clam_sb', 'clam_mb', 'mil'

Issue - State: closed - Opened by mhoibo 3 months ago - 1 comment

#262 - Allow patching using magnification

Pull Request - State: closed - Opened by haydenych 3 months ago

#261 - 1 to 1 correspondence between slide (*.svs) and patches/stitches???

Issue - State: closed - Opened by qserenali 4 months ago - 1 comment

#259 - About the custom_downsample parameter in extract_feature_fp.py

Issue - State: closed - Opened by H-Q-N 4 months ago - 1 comment
Labels: question

#258 - Atypia

Pull Request - State: closed - Opened by wtprew 4 months ago

#257 - The first step to get the segment ， the margin is too large

Issue - State: closed - Opened by simzhangbest 4 months ago - 1 comment
Labels: question

#256 - Attention maps for multiple predictions

Issue - State: closed - Opened by otto863 4 months ago - 1 comment
Labels: question

#255 - Extracting Raw Patches (.jpg / ./png)

Issue - State: closed - Opened by bryanwong17 4 months ago

#254 - Heatmaps are patchy and not smooth

Issue - State: closed - Opened by rohith2011 5 months ago - 1 comment

#252 - heatmap

Issue - State: closed - Opened by suminwei 5 months ago - 1 comment

#250 - vsi format

Issue - State: closed - Opened by homadnmr 6 months ago - 1 comment

#249 - expand sdpc format

Issue - State: closed - Opened by lingxitong 6 months ago - 4 comments

#248 - Problem running split in CONCH/CLAM environment

Issue - State: closed - Opened by suminwei 6 months ago - 2 comments

#247 - Adapting data loader to multi class & multi label

Issue - State: closed - Opened by Fel1xJulian 6 months ago - 1 comment
Labels: good first issue, question

#246 - KeyError: "Unable to synchronously open attribute (can't locate attribute: 'patch_level')"

Issue - State: closed - Opened by MarioPaps 7 months ago - 1 comment
Labels: question

#245 - Datasets in configuration file and GPU Training Step

Issue - State: closed - Opened by rohith2011 7 months ago - 1 comment

#244 - added missing args & correct import of eval_transforms

Pull Request - State: closed - Opened by shubhaminnani 7 months ago - 1 comment

#243 - Questions about threshold parameters

Issue - State: closed - Opened by huha149 7 months ago - 1 comment
Labels: question

#242 - Segmentation parameters for WSI with partially black background

Issue - State: closed - Opened by Fel1xJulian 7 months ago - 1 comment

#238 - New code breaks CLAM_MB model

Issue - State: closed - Opened by zhanghaoyue 7 months ago - 1 comment

#237 - GPU usage with the new version

Issue - State: closed - Opened by gusSCIMOV 7 months ago - 3 comments

#236 - Unable to import 'datasets.dataset_generic'

Issue - State: closed - Opened by gusSCIMOV 7 months ago - 2 comments

#235 - add support for UNI/CONCH

Pull Request - State: closed - Opened by fedshyvana 7 months ago

#234 - Error during segmentation

Issue - State: closed - Opened by suminwei 7 months ago

#233 - Running CLAM model on independent test data

Issue - State: closed - Opened by suminwei 8 months ago

#232 - The code really needs fixing

Issue - State: closed - Opened by onbigion13 8 months ago - 2 comments

#231 - About parameters in process_list.autogen.csv

Issue - State: closed - Opened by syy-create 8 months ago - 1 comment

#230 - For binary sub-disease classification

Issue - State: closed - Opened by pxliang 9 months ago - 1 comment

#229 - Problems encountered during feature extraction

Issue - State: closed - Opened by DuWei0126 9 months ago - 1 comment

#227 - Extracting features problem with h5 files

Issue - State: closed - Opened by BioCoderR 9 months ago - 1 comment

#225 - Many Nan values in the extracted feature

Issue - State: closed - Opened by folkaholic 10 months ago - 7 comments

#224 - Only one GPU during training

Issue - State: closed - Opened by YinZhe0412 10 months ago - 4 comments

#223 - Some artifacts are identified as tissue regions

Issue - State: closed - Opened by huha149 10 months ago - 2 comments

#222 - What data types can be processed

Issue - State: closed - Opened by syy-create 10 months ago - 4 comments

#221 - fixing typos in Readme

Pull Request - State: open - Opened by Borda 10 months ago - 2 comments

#220 - Seeking Advice: Low Accuracy in CLAM Training on CAMELYON16 Dataset

Issue - State: closed - Opened by ACNicotine 11 months ago - 1 comment

#219 - `custom_downsample` specification flipped for heatmaps?

Issue - State: closed - Opened by vipulnj 11 months ago - 3 comments

#218 - Threshold adjustment in preprocessing stage

Issue - State: closed - Opened by ACNicotine 11 months ago - 1 comment

#217 - Running eval.py

Issue - State: closed - Opened by suminwei 11 months ago - 4 comments

#216 - Failed to install using clam.yaml due to conflicts

Issue - State: closed - Opened by l-cli 11 months ago - 2 comments

#215 - Issue running create_heatmaps.py

Issue - State: closed - Opened by suminwei 11 months ago - 2 comments

#214 - Some WSI cannot be segmented

Issue - State: closed - Opened by Ysc-shark 12 months ago - 1 comment

#213 - Run your own dataset

Issue - State: closed - Opened by Tanhongyun 12 months ago - 2 comments

#212 - Issue running main.py

Issue - State: closed - Opened by suminwei about 1 year ago - 2 comments

#211 - The problem of uniform magnification

Issue - State: closed - Opened by LiuJin629 about 1 year ago - 2 comments

#210 - ".ndpi" type WSI

Issue - State: closed - Opened by LiuJin629 about 1 year ago - 7 comments

#209 - Poor performance

Issue - State: closed - Opened by AnitaGoro about 1 year ago - 1 comment

#208 - How to set the parameters when converting from 40X WSI to 20X WSI

Issue - State: closed - Opened by YinZhe0412 about 1 year ago - 2 comments

#207 - difference among seg_level, patch_level and custom_downsample about TCGA-BRCA

Issue - State: closed - Opened by ljhOfGithub about 1 year ago - 7 comments

#206 - minor fix for create_patches_fp.py saving .h5 files to image source directory

Issue - State: closed - Opened by VictorLee94 about 1 year ago - 2 comments

#205 - positional information restore

Issue - State: closed - Opened by ljhOfGithub about 1 year ago

#204 - Running CLAM without Feature Extraction

Issue - State: closed - Opened by VictorLee94 about 1 year ago

#203 - I want to use your tumor segmentation pretrained model

Issue - State: closed - Opened by AnitaGoro about 1 year ago - 1 comment

#202 - CLAM main.py failes

Issue - State: closed - Opened by eladzis about 1 year ago - 4 comments

#200 - HeatMap

Issue - State: closed - Opened by wxyz-wjx about 1 year ago - 1 comment

#199 - Update WholeSlideImage.py

Pull Request - State: closed - Opened by scjjb over 1 year ago

#198 - about TCGA-A7-A0CD-01Z-00-DX2.609CED8D-5947-4753-A75B-73A8343B47EC.svs

Issue - State: closed - Opened by ljhOfGithub over 1 year ago - 1 comment

#197 - problem about N fold cross validation using create_split_seq.py

Issue - State: closed - Opened by ljhOfGithub over 1 year ago - 1 comment

#195 - label of instances

Issue - State: closed - Opened by ravigupta131 over 1 year ago - 1 comment

#194 - fix:score2percentile()

Pull Request - State: open - Opened by ljhOfGithub over 1 year ago - 2 comments

#193 - Refactor: Move clam project to subdirectory

Pull Request - State: closed - Opened by dagoPA over 1 year ago - 2 comments

#192 - Error in plotting heatmap

Issue - State: closed - Opened by dawalisi over 1 year ago - 4 comments

#190 - Conda installation error with PyTorch

Issue - State: closed - Opened by jonasmrr over 1 year ago - 7 comments

#185 - Image Augmentation

Issue - State: closed - Opened by nabilapuspit over 1 year ago - 4 comments

#183 - Problem with process_contour function when contour is None

Issue - State: closed - Opened by loic-lb over 1 year ago

#180 - A little question in /models/model_clam.py

Issue - State: closed - Opened by ShiCrazy over 1 year ago

#179 - Use feature extraction files to train a ML model

Issue - State: closed - Opened by Tato14 over 1 year ago - 2 comments

#165 - Patch magnification

Issue - State: closed - Opened by bryanwong17 almost 2 years ago - 2 comments

#163 - How to downsample from 40x to 20x using create_patches_fp when level 1 is 4

Issue - State: closed - Opened by maduc7 almost 2 years ago - 7 comments

#159 - How to maintain reference patch size of 256x256

Issue - State: closed - Opened by Tejussurendran about 2 years ago - 2 comments

#151 - "--patch" in create_patches.py and create_patch_fp.py

Issue - State: closed - Opened by luojing1030 about 2 years ago - 3 comments

#145 - magnitude parameter

Issue - State: open - Opened by Bontempogianpaolo1 about 2 years ago - 6 comments

#135 - inst_label

Issue - State: closed - Opened by Akihiko0123 over 2 years ago - 5 comments

#130 - Excluding tissue patch covered in pen marker?

Issue - State: closed - Opened by rushin682 over 2 years ago - 4 comments

#123 - Normal Lung Tissue

Issue - State: closed - Opened by GeorgeBatch over 2 years ago - 5 comments

#118 - Upgrade file reader to tifffile

Issue - State: open - Opened by pcicales over 2 years ago - 7 comments

#115 - Interpretation of the AUC in a summary result (reproducing RCC)

Issue - State: closed - Opened by omniaalwazzan over 2 years ago - 16 comments

#103 - Custom ResNet vs Torchvision Resnet

Issue - State: closed - Opened by GeorgeBatch over 2 years ago - 7 comments

#100 - Bad sensitivity in independent testing dataset

Issue - State: closed - Opened by MohamedOmar2020 almost 3 years ago - 4 comments