Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / BodenmillerGroup/steinbock issues and pull requests

#270 - Measure intensities of user-defined loci

Issue - State: closed - Opened by Shhsvri 23 days ago - 1 comment

#269 - Different signal intensities for the same ROI

Issue - State: closed - Opened by yasrod 3 months ago - 4 comments

#268 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] 3 months ago

#265 - Update build.yml to use self-hosted runner

Pull Request - State: closed - Opened by Milad4849 5 months ago

#264 - Update build.yml

Pull Request - State: closed - Opened by Milad4849 5 months ago

#263 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#262 - Update readimc to 0.7.0 + lenient parsing option

Pull Request - State: closed - Opened by matt-sd-watson 7 months ago - 2 comments

#261 - update readimc to 0.7.0 for lenient parsing

Issue - State: closed - Opened by matt-sd-watson 7 months ago

#259 - Strange invalid literal error..

Issue - State: open - Opened by paulrbuckley-kcl 7 months ago - 2 comments
Labels: bug

#258 - steinbock apps ilastik - Ilastik crashing upon startup

Issue - State: closed - Opened by Will760 7 months ago - 1 comment

#257 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago

#256 - deepcell segmenting error

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

#255 - error with preprocess imc images --hpf50

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

#254 - 1 really poor, but essential, marker with extremely high background

Issue - State: closed - Opened by FelixShore1 7 months ago - 1 comment

#253 - two sets of images with slightly different panels

Issue - State: closed - Opened by Will760 7 months ago - 4 comments

#252 - issue of Segmentation fault

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

#251 - Unable to find image 'preprocess:latest' locally error

Issue - State: closed - Opened by MAvdB-KCL 8 months ago - 1 comment

#250 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago

#249 - random forest-based segmentation using Ilastik/CellProfiler

Issue - State: closed - Opened by mjnajafpanah 8 months ago - 6 comments

#248 - preprocess imc panel Error

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

#247 - Cannot open Ilastik through steinbock apps ilastik command

Issue - State: closed - Opened by gemmawilson 9 months ago - 2 comments

#244 - External OME.TIFF file segmentation , transformed from qptiff

Issue - State: closed - Opened by alexeykb 9 months ago - 11 comments

#243 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 9 months ago

#242 - Error: No panel/.mcd/.txt file found

Issue - State: closed - Opened by icepsi23 10 months ago - 4 comments

#241 - Intensities csv labeling objects only evens

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

#240 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago

#239 - Documentation is inaccessible

Issue - State: closed - Opened by LenisLin 10 months ago

#238 - ose

Issue - State: closed - Opened by Elena983 10 months ago - 1 comment

#236 - qptiff format

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

#235 - Export AnnData error

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

#234 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#233 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#232 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#231 - Tiff Images from Leica Stellaris

Issue - State: closed - Opened by rana228 12 months ago - 4 comments

#230 - Steinbock preprocess IMC produces empty TIFF files

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

#229 - steinbock measure neighbors very slow

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

#228 - Differences in segmentation results

Issue - State: closed - Opened by DomenicoSkyWalker89 12 months ago - 12 comments

#227 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 1 year ago

#226 - Updated citation

Pull Request - State: closed - Opened by nilseling about 1 year ago - 4 comments

#225 - deepcell error

Issue - State: closed - Opened by francescaclemente about 1 year ago - 6 comments

#224 - Hot pixel filter issue

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

#223 - Mask signal discordance

Issue - State: closed - Opened by megleila about 1 year ago - 6 comments

#222 - ArrayMemoryError - 'measure_centroid_distance_neighbors'

Issue - State: closed - Opened by paulrbuckley-kcl about 1 year ago - 3 comments

#221 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#220 - Unable to detect files and directories

Issue - State: closed - Opened by alasdairball about 1 year ago - 9 comments

#219 - Could not open ilastik GUI in windows

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

#218 - Develop

Pull Request - State: open - Opened by Milad4849 over 1 year ago - 5 comments

#217 - corrected cellpose_view_cmd

Pull Request - State: closed - Opened by Milad4849 over 1 year ago

#216 - Implemented cellpose2.0 model zoo and training

Pull Request - State: closed - Opened by Milad4849 over 1 year ago - 1 comment

#215 - Develop

Pull Request - State: closed - Opened by Milad4849 over 1 year ago

#214 - Cellpose app

Pull Request - State: closed - Opened by Milad4849 over 1 year ago - 1 comment

#213 - update develop with recent changes in main (bug fixes etc)

Pull Request - State: closed - Opened by Milad4849 over 1 year ago

#212 - Enhance errmsg for misssing roi

Pull Request - State: closed - Opened by Milad4849 over 1 year ago - 3 comments

#210 - [Bug]No neighborhood Data in h5ad-files?

Issue - State: open - Opened by albert180 over 1 year ago - 1 comment
Labels: duplicate

#208 - tissuenet model support and documentation

Issue - State: open - Opened by lassedochreden over 1 year ago
Labels: documentation

#206 - Using the preprocess external option with large images

Issue - State: open - Opened by mjseignon over 1 year ago - 6 comments
Labels: bug

#205 - cytomarker panels

Issue - State: open - Opened by jwindhager over 1 year ago
Labels: enhancement

#204 - Add option to remove the first acquisition row in IMC images.

Issue - State: open - Opened by nathansteenbuck over 1 year ago - 1 comment
Labels: enhancement

#203 - Invalid number of aggregated channels

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

#202 - `--strict/--no-strict` for `steinbock preprocess imc images` command

Issue - State: open - Opened by jwindhager over 1 year ago
Labels: enhancement

#201 - TypeError - code that used to work

Issue - State: open - Opened by paulrbuckley-kcl over 1 year ago

#199 - Add a `--channels-last` option to `steinbock preprocess external`

Issue - State: open - Opened by jwindhager over 1 year ago
Labels: enhancement

#198 - Obfuscated logging in external preprocessing

Issue - State: open - Opened by jwindhager over 1 year ago
Labels: bug

#197 - ome-tiff issue

Issue - State: open - Opened by paulrbuckley-kcl over 1 year ago - 3 comments

#196 - Concatenated anndata export does not retain neighborhood information

Issue - State: open - Opened by jwindhager over 1 year ago
Labels: bug

#195 - Error when running `steinbock classify ilastik run`

Issue - State: open - Opened by nilseling over 1 year ago - 4 comments

#194 - expand_mask(mask, distance)

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

#193 - Lineage-aware ground-truth segmentation using deepcell within steinbock

Issue - State: closed - Opened by megleila over 1 year ago - 3 comments

#192 - Segmentation fault in python package

Issue - State: open - Opened by ynanli over 1 year ago - 6 comments

#190 - Enhanced error handling of corrupted IMC files with no recovery txt

Pull Request - State: closed - Opened by Milad4849 over 1 year ago - 3 comments

#189 - Scaling and renormalisation during cell segmentation

Issue - State: closed - Opened by BonoC over 1 year ago - 6 comments

#188 - Docker image failing at Ilastik step

Issue - State: closed - Opened by eleonore-schneeg over 1 year ago - 11 comments

#187 - Releasing 0.16.1 failed, build workflow potentially broken?

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

#186 - segmentation error by deepcell for large tiff

Issue - State: closed - Opened by dingxm over 1 year ago - 8 comments

#185 - cellpose not included in steinbock:0.16.0

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

#184 - Print specific Error message for missing ROI

Issue - State: closed - Opened by nathansteenbuck over 1 year ago - 2 comments
Labels: enhancement

#182 - OME preprocessing hotfix

Pull Request - State: closed - Opened by jwindhager over 1 year ago - 1 comment
Labels: bug

#181 - Converting external .ome.tiff file

Issue - State: closed - Opened by mjseignon over 1 year ago - 1 comment
Labels: bug

#179 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#177 - Error message when executing "steinbock measure intensities"

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

#175 - Unifying how panel column datatypes are handeled & adding cellpose 2.0 support

Pull Request - State: closed - Opened by Milad4849 almost 2 years ago - 3 comments

#173 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago

#172 - Handover (no release)

Pull Request - State: closed - Opened by jwindhager almost 2 years ago - 1 comment

#171 - Enable memory mapping by default

Issue - State: open - Opened by jwindhager almost 2 years ago
Labels: enhancement

#170 - Add `steinbock export zarr` command

Issue - State: open - Opened by jwindhager almost 2 years ago
Labels: enhancement

#169 - Potentially introduce `steinbock preprocess ome/zarr panel/images` commands

Issue - State: open - Opened by jwindhager almost 2 years ago
Labels: enhancement

#168 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago

#167 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago

#166 - Improve DeepCell/Mesmer documentation

Pull Request - State: closed - Opened by jwindhager almost 2 years ago - 7 comments
Labels: documentation

#165 - prepare handover

Pull Request - State: closed - Opened by jwindhager almost 2 years ago

#164 - v0.16.0

Pull Request - State: closed - Opened by jwindhager almost 2 years ago - 1 comment
Labels: bug, documentation, enhancement

#163 - Inconsistent number of channels when using DeepCell/Mesmer segmentation

Issue - State: closed - Opened by yiqiaochen7 almost 2 years ago - 3 comments
Labels: support

#161 - Implement mosaic overlap for segmentation

Issue - State: open - Opened by jwindhager almost 2 years ago
Labels: enhancement, good first issue