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BodenmillerGroup
/
steinbock
A toolkit for processing multiplexed tissue images
https://bodenmillergroup.github.io/steinbock
MIT License
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14
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Enhance errmsg for misssing roi
#212
Milad4849
closed
11 months ago
3
[Bug]No neighborhood Data in h5ad-files?
#210
albert180
opened
11 months ago
1
tissuenet model support and documentation
#208
lassedochreden
opened
11 months ago
0
Maximum amount of segmented cells bounded from segmentation output file format (16-bit unsigned integer TIFF images)
#207
asom
opened
11 months ago
3
Using the preprocess external option with large images
#206
mjseignon
opened
1 year ago
6
cytomarker panels
#205
jwindhager
opened
1 year ago
0
Add option to remove the first acquisition row in IMC images.
#204
nathansteenbuck
opened
1 year ago
1
Invalid number of aggregated channels
#203
giuliospinozzi
closed
1 year ago
1
`--strict/--no-strict` for `steinbock preprocess imc images` command
#202
jwindhager
opened
1 year ago
0
TypeError - code that used to work
#201
paulrbuckley-kcl
opened
1 year ago
0
Add a `--channels-last` option to `steinbock preprocess external`
#199
jwindhager
opened
1 year ago
0
Obfuscated logging in external preprocessing
#198
jwindhager
opened
1 year ago
0
ome-tiff issue
#197
paulrbuckley-kcl
opened
1 year ago
3
Concatenated anndata export does not retain neighborhood information
#196
jwindhager
opened
1 year ago
0
Error when running `steinbock classify ilastik run`
#195
nilseling
opened
1 year ago
4
expand_mask(mask, distance)
#194
eleonore-schneeg
closed
7 months ago
1
Lineage-aware ground-truth segmentation using deepcell within steinbock
#193
megleila
closed
1 year ago
3
Segmentation fault in python package
#192
ynanli
opened
1 year ago
6
Update the CellProfiler pipeline for pixel classification based segmentation
#191
nilseling
opened
1 year ago
5
Enhanced error handling of corrupted IMC files with no recovery txt
#190
Milad4849
closed
11 months ago
3
Scaling and renormalisation during cell segmentation
#189
BonoC
closed
1 year ago
6
Docker image failing at Ilastik step
#188
eleonore-schneeg
closed
1 year ago
11
Releasing 0.16.1 failed, build workflow potentially broken?
#187
jwindhager
closed
1 year ago
2
segmentation error by deepcell for large tiff
#186
dingxm
closed
7 months ago
8
cellpose not included in steinbock:0.16.0
#185
dingxm
closed
1 year ago
4
Print specific Error message for missing ROI
#184
nathansteenbuck
closed
7 months ago
2
OME preprocessing hotfix
#182
jwindhager
closed
1 year ago
1
Converting external .ome.tiff file
#181
mjseignon
closed
1 year ago
1
The steinbock.sh script downloads the IMCWorkflow.ilp file and the ilastik folder, which are used to run the entire steinbock analysis process. How did these two files come about
#180
Masteryuanli
closed
1 year ago
0
[pre-commit.ci] pre-commit autoupdate
#179
pre-commit-ci[bot]
closed
11 months ago
0
Error message when executing "steinbock measure intensities"
#177
marleneweiss
closed
1 year ago
2
Unifying how panel column datatypes are handeled & adding cellpose 2.0 support
#175
Milad4849
closed
11 months ago
3
[pre-commit.ci] pre-commit autoupdate
#173
pre-commit-ci[bot]
closed
1 year ago
0
Handover (no release)
#172
jwindhager
closed
1 year ago
1
Enable memory mapping by default
#171
jwindhager
opened
1 year ago
0
Add `steinbock export zarr` command
#170
jwindhager
opened
1 year ago
0
Potentially introduce `steinbock preprocess ome/zarr panel/images` commands
#169
jwindhager
opened
1 year ago
0
[pre-commit.ci] pre-commit autoupdate
#168
pre-commit-ci[bot]
closed
1 year ago
0
[pre-commit.ci] pre-commit autoupdate
#167
pre-commit-ci[bot]
closed
1 year ago
0
Improve DeepCell/Mesmer documentation
#166
jwindhager
closed
1 year ago
7
prepare handover
#165
jwindhager
closed
1 year ago
0
v0.16.0
#164
jwindhager
closed
1 year ago
1
Inconsistent number of channels when using DeepCell/Mesmer segmentation
#163
yiqiaochen7
closed
1 year ago
3
Implement mosaic overlap for segmentation
#161
jwindhager
opened
1 year ago
0
Update Docker setup instructions
#160
jwindhager
closed
1 year ago
0
Document & test use with singularity
#159
jwindhager
opened
1 year ago
7
Error when trying to execute "Image visualization" in napari.ipynb
#158
marleneweiss
closed
1 year ago
5
Completely black masks from deepcell
#157
paulrbuckley-kcl
closed
1 year ago
5
In entrypoint, only call fixuid if running in Docker
#156
jwindhager
closed
1 year ago
0
Can't run with singularity
#155
paulrbuckley-kcl
closed
1 year ago
11
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