BodenmillerGroup/steinbock issues and pull requests

#160 - Update Docker setup instructions

Issue - State: closed - Opened by jwindhager almost 2 years ago
Labels: documentation

#159 - Document & test use with singularity

Issue - State: open - Opened by jwindhager almost 2 years ago - 7 comments
Labels: documentation, good first issue

#158 - Error when trying to execute "Image visualization" in napari.ipynb

Issue - State: closed - Opened by marleneweiss almost 2 years ago - 5 comments
Labels: support

#157 - Completely black masks from deepcell

Issue - State: closed - Opened by paulrbuckley-kcl almost 2 years ago - 5 comments
Labels: support

#156 - In entrypoint, only call fixuid if running in Docker

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

#155 - Can't run with singularity

Issue - State: closed - Opened by paulrbuckley-kcl almost 2 years ago - 11 comments
Labels: support

#154 - Deepcell command not found

Issue - State: closed - Opened by sshin48 about 2 years ago - 7 comments
Labels: support

#153 - Segmentation issues

Issue - State: closed - Opened by KHALILISAEED about 2 years ago - 7 comments
Labels: support

#152 - AMD64

Issue - State: closed - Opened by cuiriouscancerscientist about 2 years ago - 1 comment
Labels: duplicate

#151 - intensities/regionprops measurement of potentially corrupted TIFF files crashes with empty error message

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

#150 - IMC recovery from txt file is potentially broken

Issue - State: closed - Opened by jwindhager about 2 years ago - 1 comment
Labels: bug, verify

#149 - Steinbock container keeps exiting

Issue - State: closed - Opened by cuiriouscancerscientist about 2 years ago - 8 comments
Labels: support

#148 - DeepCell input data

Issue - State: closed - Opened by rahilgholami about 2 years ago - 4 comments
Labels: support

#147 - v0.15.0

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

#146 - WARNING steinbock - Failed to relabel image with shape (1, 12997, 25785)

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

#145 - [Help] ilastik batch process step cannot find `pixel_classifier.ilp`

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

#143 - Can't locate Ilastik

Issue - State: closed - Opened by tryggest about 2 years ago - 3 comments
Labels: support

#142 - Support .tif file extension

Issue - State: closed - Opened by jwindhager over 2 years ago
Labels: enhancement, wontfix

#141 - Make ZIP extraction accessible

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

#140 - Factor out image metadata creation

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

#139 - Factor out DeepCell segmentation stack creation

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

#138 - Using 'postprocess_kwargs=' with steinbock deepcell segment?

Issue - State: closed - Opened by Pancreas-Pratik over 2 years ago - 4 comments
Labels: documentation, support

#137 - Steinbock issue with starting ilastik

Issue - State: closed - Opened by StiThor over 2 years ago - 5 comments
Labels: support

#136 - Error in "steinbock export histocat"

Issue - State: closed - Opened by jparkinson375 over 2 years ago - 2 comments
Labels: bug

#135 - Examples

Pull Request - State: open - Opened by jwindhager over 2 years ago - 6 comments
Labels: documentation

#134 - v0.14.2

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

#133 - Exclude hidden files from processing

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

#132 - Running with -e STEINBOCK_MASK_DTYPE=uint32 flag error

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

#131 - automatically detect uint type in io.py

Issue - State: closed - Opened by jinyancool over 2 years ago - 5 comments
Labels: support

#130 - Reproducibility across releases

Issue - State: closed - Opened by nilseling over 2 years ago - 1 comment
Labels: support

#129 - v0.14.1

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

#128 - steinbock wheel is broken

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

#127 - Fix CUDA build

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

#126 - v0.14.0

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

#125 - Upgrade to DeepCell 0.12.0

Issue - State: closed - Opened by jwindhager over 2 years ago
Labels: enhancement

#124 - Neighbors measurements are broken

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

#123 - Custom exceptions

Issue - State: closed - Opened by jwindhager over 2 years ago
Labels: enhancement

#122 - Use logging instead of click.echo

Issue - State: closed - Opened by jwindhager over 2 years ago
Labels: enhancement

#121 - Error when building image from Dockerfile

Issue - State: closed - Opened by Emberwhirl over 2 years ago - 3 comments
Labels: documentation

#120 - Adding manual crops for Ilastik training

Issue - State: closed - Opened by luglilab over 2 years ago - 4 comments
Labels: support

#118 - Add cellpose support

Issue - State: closed - Opened by jwindhager over 2 years ago - 1 comment
Labels: enhancement, good first issue

#117 - docker container fills up with temporary files

Issue - State: closed - Opened by nilseling over 2 years ago
Labels: enhancement

#116 - Stitching mosaics produces empty output

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

#115 - steinbock apps ilastik

Issue - State: closed - Opened by YZYwoazzzzz over 2 years ago - 3 comments
Labels: support

#114 - What analysis can generate the file Pixel_classifier.ilp[

Issue - State: closed - Opened by DrLGB over 2 years ago - 1 comment
Labels: support

#113 - Feature request: saving images in other file formats

Issue - State: open - Opened by nilseling over 2 years ago - 5 comments
Labels: enhancement, good first issue

#112 - cellprofiler test mode-no preview window pops up

Issue - State: closed - Opened by sailseem over 2 years ago - 1 comment

#111 - Default Ilastik/CellProfiler files not shipped with PyPI releases

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

#110 - steinbock classify ilastik prepare

Issue - State: closed - Opened by sailseem over 2 years ago - 26 comments
Labels: support

#109 - Add support for 4-channel TIFFs

Issue - State: closed - Opened by jwindhager over 2 years ago
Labels: enhancement

#108 - Unsupported Number of Dimension

Issue - State: closed - Opened by lmhasse over 2 years ago - 6 comments
Labels: support

#107 - Comparison of neighbour detection to CellProfiler

Issue - State: open - Opened by nilseling almost 3 years ago - 5 comments
Labels: good first issue, verify

#106 - mask expansion

Issue - State: closed - Opened by SchulzDan almost 3 years ago - 3 comments
Labels: enhancement, good first issue

#105 - calling cellprofiler app fails in 0.13.4

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

#104 - explain docker run options

Issue - State: closed - Opened by SchulzDan almost 3 years ago
Labels: documentation

#103 - Add logging of steinbock commands

Issue - State: open - Opened by jwindhager almost 3 years ago - 2 comments
Labels: enhancement, good first issue

#102 - Error: Invalid value for '--pipe': File 'cell_measurement.cppipe' does not exist.

Issue - State: closed - Opened by nilseling almost 3 years ago - 2 comments
Labels: invalid

#101 - Error reading yaml file for postprocessing in deepcell

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

#100 - steinbock duplicates ROIs

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

#99 - v0.13.0

Pull Request - State: closed - Opened by jwindhager almost 3 years ago
Labels: bug, documentation, enhancement

#98 - tensorflow not supported on Apple M1 chips

Issue - State: open - Opened by lassedochreden almost 3 years ago - 15 comments
Labels: enhancement, wontfix

#97 - Docs don't show properly in Firefox on Mac

Issue - State: closed - Opened by jwindhager almost 3 years ago - 1 comment
Labels: bug, documentation, invalid

#96 - Fix panel.csv in steinbock preprocess imc panel (from .txt), multiple rows per channel + column name incompatibility w/ CATALYST

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

GitHub / BodenmillerGroup/steinbock issues and pull requests