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BodenmillerGroup
/
ImcSegmentationPipeline
A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
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1_prepare_ilastik.cppipe pipeline not working
#140
akedarg
opened
1 month ago
6
Error when creating spatial experiment object from IMC segmentation pipeline: 'Could not guess delimiter'.
#139
AnanyaBhalla
closed
1 month ago
2
Error in 3_measure_mask.cppipe
#138
Acaro12
closed
4 months ago
4
Corrupt MCD file - using .txt instead
#137
Acaro12
closed
5 months ago
4
windows zip file compression type not recognized
#136
arcolombo
opened
6 months ago
0
TIFF output all black
#135
alyoung85
closed
7 months ago
4
Jupyter-lab did not open Jupyter notebook
#134
Ewaoluwa1
closed
11 months ago
5
Updated XLSX to CSV download
#133
nilseling
closed
1 year ago
0
Unable to load Ilastik crop pipeline file to CellProfiler
#132
CodeCheong
closed
1 year ago
3
Numpy float or unsigned integer in TIFF images
#131
petesfew
closed
5 months ago
3
Presence of undefined channels during conversion from MCD to ome-TIFF
#130
petesfew
closed
1 year ago
2
single-cell expression data
#129
Shawnmhy
closed
1 year ago
1
Error“Generate image stacks for downstream analyses”
#128
HouPB
closed
1 year ago
13
Nd145 not in list error when generating image stacks
#127
Yanira1208
closed
1 year ago
5
Allow handling of MCD files with missing channel labels
#126
nilseling
closed
1 year ago
0
Pre-processing error
#125
ssaintsoon
closed
1 year ago
8
Error installing conda environment
#124
rachel662
closed
1 year ago
7
Fixes issue #122, Switch to MCDFile.schema_xml to keep up with readimc.
#123
Milad4849
closed
1 year ago
2
Switch use of readimc in pipeline
#122
nilseling
closed
1 year ago
1
Make pipeline compatible with unlabeled channels
#121
jwindhager
closed
1 year ago
1
Image Stacks Generation - Key Error
#120
Guille916
closed
1 year ago
19
Creating unique .h5 files for Ilastik from ImcSegmentationPipeline Jupyter notebook
#119
chinoeke
closed
1 year ago
2
Error while loading summarizestack
#118
svelagala007
closed
1 year ago
3
Cell segmentation in placental cells.
#117
svelagala007
closed
1 year ago
2
metadata acquisition
#116
Bunmi0616
closed
1 year ago
2
Cell In[6], line 1 the paths with the ziped acquisition files ^ SyntaxError: invalid syntax
#115
svelagala007
closed
1 year ago
7
Getting AttributeErrors when running section [6]
#114
JaydenGittens
closed
1 year ago
13
use channel name as label for unlabeled channels
#113
jwindhager
closed
1 year ago
11
Error "FileNotFound" in the last step
#112
aleixrius
closed
1 year ago
4
Avoid processing of hidden files
#111
nilseling
closed
1 year ago
12
ValueError : No object to concatenate (Convert .mcd files to .ome.tiff files)
#110
Sudhirkumarchauhan
closed
1 year ago
23
exclude dotfiles (closes #94)
#109
jwindhager
closed
1 year ago
0
location of conda_imctools.yml
#108
fbenedett
closed
1 year ago
2
Question on the identifySecondaryObject in the CellProfiler Pipeline (general question )
#107
arcolombo
closed
1 year ago
4
Error imcsegpipe.extract_mcd_file can not read panorama
#106
arcolombo
closed
1 year ago
2
Error in open 1_prepare_ilastik.cppipe
#105
Byronxy
closed
1 year ago
8
No module named 'imcsegpipe' error
#104
honeybee-224
closed
1 year ago
9
Problems with script in Anaconda Navigator (jupyer)
#103
StiThor
closed
1 year ago
15
zsh:1: parse error near `-m'
#102
honeybee-224
closed
1 year ago
1
Errors setting up with example data
#101
honeybee-224
closed
1 year ago
3
imwrite() got an unexpected keyword argument 'compress'
#100
ingros
closed
2 years ago
9
Remove tifffile pinning
#99
jwindhager
closed
2 years ago
0
Select ROIs for analysis
#98
Jeffchingg
closed
2 years ago
2
SummarizeStack module cannot be loaded properly
#97
Jeffchingg
closed
2 years ago
3
BadZipFile error
#96
Jeffchingg
closed
2 years ago
2
'{sys.executable}' is not recognized; imcsegpipe not found
#95
Jeffchingg
closed
2 years ago
8
Corrupt MCD
#94
Laner
closed
1 year ago
8
Unexpected argument 'compress'
#92
Laner
closed
2 years ago
2
Hotfix xtiff/tifffile issue
#91
jwindhager
closed
2 years ago
0
write() got an unexpected keyword argument 'compress'
#90
olivierbortolotti
closed
2 years ago
4
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