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BodenmillerGroup
/
steinbock
A toolkit for processing multiplexed tissue images
https://bodenmillergroup.github.io/steinbock
MIT License
49
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14
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Can't run with singularity
#155
paulrbuckley-kcl
closed
1 year ago
11
Deepcell command not found
#154
sshin48
closed
1 year ago
7
Segmentation issues
#153
KHALILISAEED
closed
1 year ago
7
AMD64
#152
cuiriouscancerscientist
closed
1 year ago
1
intensities/regionprops measurement of potentially corrupted TIFF files crashes with empty error message
#151
jwindhager
closed
1 year ago
2
IMC recovery from txt file is potentially broken
#150
jwindhager
closed
1 year ago
1
Steinbock container keeps exiting
#149
cuiriouscancerscientist
closed
1 year ago
8
DeepCell input data
#148
rahilgholami
closed
1 year ago
4
v0.15.0
#147
jwindhager
closed
1 year ago
1
WARNING steinbock - Failed to relabel image with shape (1, 12997, 25785)
#146
nilseling
closed
1 year ago
0
[Help] ilastik batch process step cannot find `pixel_classifier.ilp`
#145
Mr-Milk
closed
1 year ago
2
Can't locate Ilastik
#143
tryggest
closed
1 year ago
3
Support .tif file extension
#142
jwindhager
closed
1 year ago
0
Make ZIP extraction accessible
#141
jwindhager
closed
2 years ago
1
Factor out image metadata creation
#140
jwindhager
closed
2 years ago
1
Factor out DeepCell segmentation stack creation
#139
jwindhager
closed
2 years ago
1
Using 'postprocess_kwargs=' with steinbock deepcell segment?
#138
Pancreas-Pratik
closed
2 years ago
4
Steinbock issue with starting ilastik
#137
StiThor
closed
2 years ago
5
Error in "steinbock export histocat"
#136
jparkinson375
closed
1 year ago
2
Examples
#135
jwindhager
opened
2 years ago
6
v0.14.2
#134
jwindhager
closed
2 years ago
0
Exclude hidden files from processing
#133
nilseling
closed
2 years ago
0
Running with -e STEINBOCK_MASK_DTYPE=uint32 flag error
#132
leonorss
closed
2 years ago
2
automatically detect uint type in io.py
#131
jinyancool
closed
2 years ago
5
Reproducibility across releases
#130
nilseling
closed
2 years ago
1
v0.14.1
#129
jwindhager
closed
2 years ago
0
steinbock wheel is broken
#128
jwindhager
closed
2 years ago
0
Fix CUDA build
#127
jwindhager
closed
2 years ago
0
v0.14.0
#126
jwindhager
closed
2 years ago
0
Upgrade to DeepCell 0.12.0
#125
jwindhager
closed
2 years ago
0
Neighbors measurements are broken
#124
jwindhager
closed
2 years ago
0
Custom exceptions
#123
jwindhager
closed
2 years ago
0
Use logging instead of click.echo
#122
jwindhager
closed
2 years ago
0
Error when building image from Dockerfile
#121
Emberwhirl
closed
1 year ago
3
Adding manual crops for Ilastik training
#120
luglilab
closed
2 years ago
4
Add cellpose support
#118
jwindhager
closed
1 year ago
1
docker container fills up with temporary files
#117
nilseling
closed
1 year ago
0
Stitching mosaics produces empty output
#116
lgeistlinger
closed
1 year ago
4
steinbock apps ilastik
#115
YZYwoazzzzz
closed
2 years ago
3
What analysis can generate the file Pixel_classifier.ilp[
#114
DrLGB
closed
2 years ago
1
Feature request: saving images in other file formats
#113
nilseling
opened
2 years ago
5
cellprofiler test mode-no preview window pops up
#112
sailseem
closed
2 years ago
1
Default Ilastik/CellProfiler files not shipped with PyPI releases
#111
jwindhager
closed
2 years ago
0
steinbock classify ilastik prepare
#110
sailseem
closed
2 years ago
26
Add support for 4-channel TIFFs
#109
jwindhager
closed
1 year ago
0
Unsupported Number of Dimension
#108
lmhasse
closed
2 years ago
6
Comparison of neighbour detection to CellProfiler
#107
nilseling
opened
2 years ago
5
mask expansion
#106
SchulzDan
closed
1 year ago
3
calling cellprofiler app fails in 0.13.4
#105
SchulzDan
closed
2 years ago
1
explain docker run options
#104
SchulzDan
closed
1 year ago
0
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