mahmoodlab/CLAM issues and pull requests

#99 - Openslides or openslide?

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

#98 - Black foreground after `segment` and pixel garbled after `stitch`

Issue - State: closed - Opened by pzSuen almost 3 years ago - 2 comments

#97 - OpenSlideError during feature extraction

Issue - State: closed - Opened by Dikec almost 3 years ago - 10 comments

#96 - extracting ROIs and preprocessing WSI image for graph neural network

Issue - State: closed - Opened by liuxiaoping2020 almost 3 years ago - 2 comments

#95 - Problem of getting threshold of high/low attention score and create patches problem

Issue - State: closed - Opened by yuechen9 almost 3 years ago - 1 comment

#94 - Interpreting summary results

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

#93 - (Old Issue #79) Patches and Stitches folder empty but images appear in masks

Issue - State: closed - Opened by dgonzMD almost 3 years ago - 2 comments

#92 - Questions about RCC WSI dataset

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

#91 - difference among `seg_level`, `patch_level` and `custom_downsample`

Issue - State: closed - Opened by RuixiangZhao almost 3 years ago - 2 comments

#90 - Datatype comparison bug 2021-12-01

Pull Request - State: closed - Opened by andrew-weisman almost 3 years ago - 2 comments

#89 - cv2.error: OpenCV(4.5.4-dev) :-1: error: (-5:Bad argument) in function 'pointPolygonTest'

Issue - State: closed - Opened by RuixiangZhao almost 3 years ago - 2 comments

#88 - How to generate csvs in dataset_csv?

Issue - State: closed - Opened by berooo almost 3 years ago - 1 comment

#87 - Layer interrogation

Issue - State: closed - Opened by qinghezeng almost 3 years ago - 2 comments

#86 - Using the Pipeline on MRXS format Whole Slide Images

Issue - State: closed - Opened by tarquo23 almost 3 years ago - 2 comments

#85 - Pytorch

Pull Request - State: closed - Opened by sbutcher almost 3 years ago

#84 - patch black box problem.

Issue - State: closed - Opened by cook-kuk almost 3 years ago - 3 comments

#83 - segmentation results of TCGA data

Issue - State: closed - Opened by JunMa11 about 3 years ago - 2 comments

#82 - Feature Extraction step stopping with text "Killed"

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

#81 - Questions about using CLAM software

Issue - State: closed - Opened by hjafar about 3 years ago - 1 comment

#80 - Patch filtering

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

#79 - Patches and Stitches folder empty but images appear in masks

Issue - State: closed - Opened by DeepLearningCoder about 3 years ago - 13 comments

#78 - Too large for successful segmentation and aborted

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

#77 - Catching writer exception in core_utils.py

Issue - State: closed - Opened by tabmoo about 3 years ago - 1 comment

#76 - Artifact in heatmap results

Issue - State: closed - Opened by dkoen over 3 years ago - 1 comment

#75 - Empty filtered coordinates when running create_heatmaps.py

Issue - State: closed - Opened by dkoen over 3 years ago - 12 comments

#74 - fix typo in create_heatmaps.py

Pull Request - State: closed - Opened by keithcallenberg over 3 years ago - 1 comment

#73 - Update import of smooth-topk

Pull Request - State: closed - Opened by keithcallenberg over 3 years ago

#72 - Patching on microscopy images

Issue - State: closed - Opened by tienn2 over 3 years ago - 2 comments

#71 - The "flaw" in stiches

Issue - State: closed - Opened by YohnGuan over 3 years ago - 2 comments

#70 - Typo in create_heatmaps()

Issue - State: closed - Opened by jamesdolezal over 3 years ago - 1 comment

#69 - Feature extraction speed problem.

Issue - State: closed - Opened by YohnGuan over 3 years ago - 4 comments

#68 - CLAM workflow without test set

Issue - State: closed - Opened by andrewsris over 3 years ago - 2 comments

#67 - Custom default segmentation visualization parameter, vis_level

Issue - State: closed - Opened by Hokiee over 3 years ago - 2 comments

#66 - Minor typo fix in readme

Pull Request - State: closed - Opened by keithcallenberg over 3 years ago - 1 comment

#65 - ROC curves in paper

Issue - State: closed - Opened by yyyzzzhao over 3 years ago - 2 comments

#64 - Error while running create_heatmaps.py --> ValueError: ctypes objects containing pointers cannot be pickled

Issue - State: closed - Opened by AlmashAlam over 3 years ago - 2 comments

#63 - Heatmap interpretation problem

Issue - State: closed - Opened by tienn2 over 3 years ago - 1 comment

#62 - Issue reproducing same results as that of the first training

Issue - State: closed - Opened by qinghezeng over 3 years ago - 2 comments

#61 - Inconsistent Tissue Segmentation

Issue - State: closed - Opened by artemi8 over 3 years ago - 2 comments

#60 - Heatmap greyscale issue

Issue - State: closed - Opened by andymckenzie over 3 years ago - 1 comment

#59 - Heatmap visualization

Issue - State: closed - Opened by AishwaryaAllada over 3 years ago - 1 comment

#58 - Stylizing some of the arguments for patching + segmentation in the README

Pull Request - State: closed - Opened by Richarizardd over 3 years ago

#57 - Feature extraction

Issue - State: closed - Opened by jjjjjjiayx over 3 years ago - 1 comment

#56 - Clam_sb

Issue - State: closed - Opened by mayurmallya over 3 years ago - 2 comments

#55 - Camelyon17 and Camelyon16 Training Data

Issue - State: closed - Opened by Ajaz-Ahmad over 3 years ago - 1 comment

#54 - Loading pre-trained models

Issue - State: closed - Opened by tienn2 over 3 years ago - 2 comments

#53 - Visualizing the patch-level feature space

Issue - State: closed - Opened by dsouzavijeth over 3 years ago - 2 comments

#52 - Performance on CAMELYON17

Issue - State: closed - Opened by lzx325 over 3 years ago - 3 comments

#51 - Problem of Segmentation on CAMELYON17

Issue - State: closed - Opened by lzx325 over 3 years ago - 3 comments

#50 - What script to use to rebuild the output image

Issue - State: closed - Opened by Ajaz-Ahmad over 3 years ago - 1 comment

#49 - Need help in understanding the clustering step

Issue - State: closed - Opened by samKaranth over 3 years ago - 4 comments

#48 - How to resolve runtime error in `inst_eval` caused by hardcoding k_sample

Issue - State: closed - Opened by sirgarfieldc over 3 years ago - 1 comment

#47 - Does the package work for non-exclusive multi-class classification ?

Issue - State: closed - Opened by sirgarfieldc over 3 years ago - 3 comments

#46 - getting mask contours

Issue - State: closed - Opened by gabemarx over 3 years ago - 1 comment

#45 - How to extract tissue patches as .jpg files

Issue - State: closed - Opened by hesiqi1998 over 3 years ago - 2 comments

#44 - saving coords without images?

Issue - State: closed - Opened by gabemarx over 3 years ago - 2 comments

#43 - Segmentation parameter recommendations for immunohistochemical stained WSI

Issue - State: closed - Opened by gabemarx over 3 years ago - 1 comment

#42 - Proper visualization of the heatmap

Issue - State: closed - Opened by furkandurmus over 3 years ago - 1 comment

#41 - What coordinates should be handed to visHeatmap?

Issue - State: closed - Opened by stephandooper over 3 years ago - 5 comments

#40 - Visualizing attention scores?

Issue - State: closed - Opened by slee7268 over 3 years ago - 1 comment

#39 - Multi-class slide level prediction

Issue - State: closed - Opened by Dadatata-JZ over 3 years ago - 1 comment

#38 - Requesting requirements.txt file for virtualenv users

Issue - State: closed - Opened by mayurmallya over 3 years ago - 3 comments

#37 - Graceful failure

Issue - State: closed - Opened by surya-narayanan over 3 years ago - 3 comments

#36 - Issue creating env from yaml file

Issue - State: closed - Opened by surya-narayanan almost 4 years ago - 1 comment

#35 - Can this project be extended to more than 3 class classification?

Issue - State: closed - Opened by Amith1503 almost 4 years ago - 5 comments

#34 - Training in a multi-label classification setting

Issue - State: closed - Opened by guillaumejaume almost 4 years ago - 1 comment

#33 - PAIP 2019 datasets

Issue - State: closed - Opened by codingcode111 almost 4 years ago - 1 comment

#32 - Smooth vs Hard Top K Loss

Issue - State: closed - Opened by Ajaz-Ahmad almost 4 years ago - 1 comment

#31 - How do I use CLAM to create ROI heatmaps?

Issue - State: closed - Opened by sam-jennings almost 4 years ago - 1 comment

#30 - how to set the value of val_num and test_num in create_splits_seq.py using my data

Issue - State: closed - Opened by cl2227619761 almost 4 years ago - 2 comments

#29 - Format of h5 files

Issue - State: closed - Opened by samkleeman1 almost 4 years ago - 1 comment

#28 - Patch file not creating

Issue - State: closed - Opened by harikesavan almost 4 years ago - 16 comments

#27 - Segmentation Parameters for Small Tissue Content

Issue - State: closed - Opened by quincy-125 almost 4 years ago - 6 comments

#26 - For two classes case, what is the purpose of second classifier in the CLAM_SB with same data as input.

Issue - State: closed - Opened by Ajaz-Ahmad almost 4 years ago - 1 comment

#25 - Idea behind using top-k loss function

Issue - State: closed - Opened by Ajaz-Ahmad almost 4 years ago - 4 comments

#24 - Trained CLAM Models

Issue - State: closed - Opened by ebraham47 almost 4 years ago - 1 comment

#23 - Is this repo compatible with Windows operating system?

Issue - State: closed - Opened by jiajundeng almost 4 years ago - 1 comment

#22 - Format of h5 files

Issue - State: closed - Opened by samkleeman1 almost 4 years ago - 3 comments

#21 - run eval.py get TypeError

Issue - State: closed - Opened by TinnyFlames almost 4 years ago - 5 comments

#20 - Division by zero

Issue - State: closed - Opened by UsamaI000 about 4 years ago - 16 comments

#19 - What are the use of val_num, test_num at dataset.create_splits function?

Issue - State: closed - Opened by pouya-codes about 4 years ago - 1 comment

#18 - Code adaptations for tuning model

Issue - State: closed - Opened by qinghezeng about 4 years ago - 2 comments

#17 - self.wsi out of scope from patchgen?

Issue - State: closed - Opened by nazim1021 about 4 years ago - 3 comments

#16 - Using Feature Based training to detect lesion vs Normal on PANDA Dataset

Issue - State: closed - Opened by Ajaz-Ahmad about 4 years ago - 1 comment

#15 - How to disable mutual exclusivity?

Issue - State: closed - Opened by qinghezeng about 4 years ago - 4 comments

#14 - ModuleNotFoundError: No module named 'topk'

Issue - State: closed - Opened by ASKanse about 4 years ago - 5 comments

#13 - Incomplete masks

Issue - State: closed - Opened by qinghezeng about 4 years ago - 15 comments

#12 - cv2: Too many values to unpack

Issue - State: closed - Opened by ishitamed19 about 4 years ago - 10 comments

#11 - create_splits_seq val_num and test_num

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

#10 - What are opportunities for tuning the model?

Issue - State: closed - Opened by tmabraham over 4 years ago - 3 comments

#9 - Why isn't batch size an argument for main.py?

Issue - State: closed - Opened by tmabraham over 4 years ago - 10 comments

GitHub / mahmoodlab/CLAM issues and pull requests