Dana-Farber-AIOS/pathml issues and pull requests

#340 - print c_count.value Missing parentheses in call to 'print'.

Issue - State: closed - Opened by luzy05111036 almost 2 years ago - 3 comments
Labels: bug

#339 - How to train hovernet starting with semantic-level mask image?

Issue - State: open - Opened by OmarAshkar almost 2 years ago - 3 comments
Labels: enhancement

#338 - Deepcell segmentation without cytoplasm channel

Issue - State: open - Opened by jamesMo84 about 2 years ago - 1 comment
Labels: enhancement

#337 - Allow SlideData to use existing h5path files

Pull Request - State: open - Opened by tddough98 about 2 years ago

#336 - Load tiles in parallel on workers and add options to `TissueDetectionHE`

Pull Request - State: open - Opened by tddough98 about 2 years ago - 4 comments

#335 - Parameterize dtype for h5path with `SlideData` constructor

Pull Request - State: open - Opened by tddough98 about 2 years ago - 4 comments

#334 - Merge main branch into dev

Pull Request - State: closed - Opened by tddough98 about 2 years ago - 3 comments

#333 - Add action to enforce pre-commit hooks

Pull Request - State: closed - Opened by tddough98 about 2 years ago - 2 comments

#332 - Running preprocessing pipeline on Tiles object

Issue - State: open - Opened by PaulScemama about 2 years ago - 15 comments
Labels: enhancement

#331 - Can Pathml support or read in “.TMAP” formatted WSI file?

Issue - State: open - Opened by liuxiaoping2020 about 2 years ago - 1 comment
Labels: enhancement

#330 - best way to extract anndata ( h5ad ) from hdf5 file

Issue - State: open - Opened by afshinmoradi about 2 years ago - 1 comment
Labels: enhancement

#329 - Question about the StainNormalizationHE transform

Issue - State: open - Opened by ckv1110 about 2 years ago - 1 comment

#328 - SegmentMIF Assertion error issue

Issue - State: closed - Opened by ckv1110 about 2 years ago - 2 comments
Labels: bug

#327 - docs.pathml.org is down

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

#326 - annotated-dic

Issue - State: open - Opened by afshinmoradi over 2 years ago - 3 comments
Labels: enhancement

#325 - Help required : how to add metadata in pipelines

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

#324 - Error loading multiple slides in pathml

Issue - State: closed - Opened by archanabhardwaj over 2 years ago - 4 comments
Labels: bug

#323 - Error at model training step

Issue - State: closed - Opened by archanabhardwaj over 2 years ago - 1 comment
Labels: bug

#322 - question

Issue - State: closed - Opened by afshinmoradi over 2 years ago - 1 comment
Labels: bug

#321 - Running a preprocessing pipeline on a Vectra slide with 3 levels

Issue - State: closed - Opened by MohamedOmar2020 over 2 years ago - 4 comments
Labels: bug

#320 - Make error message for extract_region more informative

Pull Request - State: closed - Opened by jacob-rosenthal over 2 years ago - 1 comment

#319 - Request to access HoVerNet pre-trained model

Issue - State: closed - Opened by 99snowleopards over 2 years ago - 4 comments
Labels: enhancement

#318 - Extend QuantifyMIF to also support brightfield images

Issue - State: open - Opened by jacob-rosenthal over 2 years ago
Labels: enhancement

#317 - Rename the default kernel in docker & create intro splash page for 127.0.0.1:8888

Issue - State: open - Opened by Dana-Farber over 2 years ago - 1 comment
Labels: documentation, enhancement

#316 - Error reading the data from h5 file format

Issue - State: closed - Opened by archanabhardwaj over 2 years ago - 1 comment
Labels: question

#315 - Dask issue

Issue - State: closed - Opened by afshinmoradi over 2 years ago - 1 comment
Labels: question

#314 - pin protobuf to 3.20.1

Pull Request - State: closed - Opened by jacob-rosenthal over 2 years ago

#313 - preprocessing for ome.tif for segmentation

Issue - State: closed - Opened by jamesMo84 over 2 years ago - 1 comment
Labels: enhancement

#312 - Missing 'natsort' package

Issue - State: closed - Opened by surya-narayanan over 2 years ago - 1 comment
Labels: bug

#311 - use current year in docs

Pull Request - State: closed - Opened by jacob-rosenthal over 2 years ago - 1 comment

#310 - v2.1.0

Pull Request - State: closed - Opened by BeeGass over 2 years ago - 2 comments

#309 - don't augment test or valid splits for PanNuke

Pull Request - State: closed - Opened by jacob-rosenthal over 2 years ago - 1 comment

#308 - Preprocessing IHC

Issue - State: closed - Opened by biagio-lunit over 2 years ago - 1 comment
Labels: enhancement

#307 - HoVerNet validation and test data-loaders are using augmentations

Issue - State: closed - Opened by eyalol over 2 years ago - 5 comments
Labels: bug

#306 - Fix tiling bug

Pull Request - State: closed - Opened by jacob-rosenthal over 2 years ago - 1 comment

#305 - Tile generation fails in some cases

Issue - State: closed - Opened by jacob-rosenthal over 2 years ago
Labels: bug

#304 - Dev logging

Pull Request - State: closed - Opened by BeeGass over 2 years ago - 2 comments

#303 - Having PathML work with virtualenv by installing open-slide dependency

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

#302 - Access the array of a WSI

Issue - State: closed - Opened by surya-narayanan almost 3 years ago - 1 comment
Labels: enhancement

#301 - Update quantify mif

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 1 comment

#300 - Not clear how to update a tile

Issue - State: closed - Opened by surya-narayanan almost 3 years ago - 3 comments
Labels: question

#299 - SegmentMIF fails and causes program to hang

Issue - State: open - Opened by surya-narayanan almost 3 years ago - 4 comments
Labels: bug

#298 - Update README.md

Pull Request - State: closed - Opened by surya-narayanan almost 3 years ago - 2 comments

#297 - Error installing owing to cached version of torch

Issue - State: closed - Opened by surya-narayanan almost 3 years ago - 6 comments
Labels: bug

#296 - problem installing, owing to numpy not found

Issue - State: closed - Opened by surya-narayanan almost 3 years ago - 4 comments
Labels: bug

#295 - try removing download buttons with custom layout template

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

#294 - Clean SegmentMIF

Pull Request - State: closed - Opened by ryanccarelli almost 3 years ago - 1 comment

#293 - Passing gpu = True in segment mif doesnt use gpu

Issue - State: closed - Opened by surya-narayanan almost 3 years ago - 4 comments
Labels: bug

#292 - Show installation steps on pathml.org

Issue - State: closed - Opened by Dana-Farber almost 3 years ago - 3 comments
Labels: documentation

#291 - Not passing in a client (potentially) causes problems

Issue - State: closed - Opened by surya-narayanan almost 3 years ago - 4 comments
Labels: bug

#290 - Release 2.0.4

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 1 comment

#289 - dont use default pip version

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 1 comment

#288 - Conda env ghactions

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 2 comments

#287 - Update PanNuke dataset URL

Pull Request - State: closed - Opened by Yu-AnChen almost 3 years ago - 2 comments

#286 - properly pass image_resolution argument to mesmer model

Pull Request - State: closed - Opened by ryanccarelli almost 3 years ago - 1 comment

#285 - Storing tiles as by marker instead of a single tile

Issue - State: closed - Opened by surya-narayanan almost 3 years ago - 2 comments
Labels: enhancement

#284 - Infer backend from path

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 1 comment

#283 - Inferring backend from filepath

Issue - State: closed - Opened by jacob-rosenthal almost 3 years ago
Labels: bug

#282 - Parallelizing tiling with empty pipeline

Issue - State: open - Opened by surya-narayanan almost 3 years ago - 4 comments

#281 - Adding to h5 file

Issue - State: closed - Opened by surya-narayanan almost 3 years ago - 9 comments

#280 - Problematic frame

Issue - State: closed - Opened by surya-narayanan almost 3 years ago - 1 comment
Labels: bug

#279 - No normalize

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 1 comment

#278 - Bioformats xy ij

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 3 comments

#277 - update PathML.org wording

Issue - State: closed - Opened by Dana-Farber almost 3 years ago - 1 comment
Labels: documentation

#276 - Tile generation with BioFormatsBackend

Issue - State: closed - Opened by jacob-rosenthal almost 3 years ago
Labels: bug

#275 - Bump ipython from 7.30.1 to 7.31.1 in /docs

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#274 - Call bioformats with dtype from pipelines

Pull Request - State: closed - Opened by ryanccarelli almost 3 years ago - 1 comment

#273 - v2.0.3

Pull Request - State: closed - Opened by ryanccarelli almost 3 years ago - 1 comment

#272 - Bioformats dtype bug

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 1 comment

#271 - Bug when converting data type

Issue - State: closed - Opened by jacob-rosenthal almost 3 years ago
Labels: bug

#270 - v2.0.2

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 1 comment

#269 - Bioformats multichannel bug

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 3 comments

#268 - Fix env setup

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 1 comment

#267 - Finalize docker

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 1 comment

#265 - Fix env setup

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

#264 - Controlling the resolution of the tiling process

Issue - State: closed - Opened by surya-narayanan almost 3 years ago - 2 comments
Labels: enhancement

#261 - Issue with the new pathml version

Issue - State: closed - Opened by mdu4003 almost 3 years ago - 5 comments
Labels: bug

#259 - Resolving dependencies between PathML and Deepcell

Issue - State: closed - Opened by ryanccarelli almost 3 years ago - 8 comments
Labels: enhancement

#248 - adding prog bar to slide dataset

Pull Request - State: closed - Opened by surya-narayanan almost 3 years ago - 3 comments

#247 - Adding a prog bar to slide_dataset.run

Issue - State: closed - Opened by surya-narayanan almost 3 years ago - 1 comment
Labels: enhancement

#245 - Docker ci

Pull Request - State: closed - Opened by jacob-rosenthal almost 3 years ago - 11 comments

#230 - Logging

Issue - State: closed - Opened by ryanccarelli about 3 years ago - 4 comments
Labels: enhancement

#228 - API for running operations at lower resolution

Issue - State: open - Opened by jacob-rosenthal about 3 years ago - 2 comments

#227 - adding the Otsu threshold to SegmentMIF

Issue - State: closed - Opened by saramoein372 about 3 years ago - 5 comments

#211 - Leaking memory

Issue - State: open - Opened by surya-narayanan about 3 years ago - 6 comments
Labels: bug

#191 - magnification issue

Pull Request - State: closed - Opened by Karenxzr about 3 years ago - 1 comment
Labels: enhancement

#165 - Add channels to slidedata

Issue - State: open - Opened by ryanccarelli over 3 years ago
Labels: enhancement

#145 - Set up github actions for packaging/distribution

Issue - State: closed - Opened by ryanccarelli over 3 years ago - 2 comments
Labels: enhancement

#142 - Remove spams dependency

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

#135 - QuantifyMIF disk/memory usage

Issue - State: closed - Opened by jacob-rosenthal over 3 years ago - 1 comment
Labels: bug

#67 - CAMELYON Datasets

Issue - State: open - Opened by ryanccarelli almost 4 years ago - 2 comments

#33 - Standardize Openslide pixel resolution level

Issue - State: closed - Opened by jacob-rosenthal about 4 years ago

GitHub / Dana-Farber-AIOS/pathml issues and pull requests