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labsyspharm
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quantification
Quantification module for mcmicro
https://github.com/labsyspharm/mcmicro
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Missing version file
#51
LukasHats
closed
2 months ago
1
Release 1.6.0 failed to build
#50
kbestak
closed
2 months ago
3
Expand MCQUANT with glcm features
#49
LukasHats
opened
2 months ago
0
CommandSingleCellExtraction.py Missing
#48
hannah413
closed
4 months ago
1
Update skimage version to at least 0.23.1 to get intensity_std regionprops metric
#47
jmuhlich
closed
4 months ago
0
Update skimage.measure._regionprops.PROP_VALS when upgrading scikit-image
#46
josenimo
closed
4 months ago
3
Enable output of version number via command line
#45
FloWuenne
closed
4 months ago
0
Clean up --intensity_props docs in README
#44
jmuhlich
closed
1 year ago
1
Added function for summing intensity values.
#43
FloWuenne
closed
1 year ago
4
Added .gitpod.yml to launch gitpod with quantification container.
#42
FloWuenne
closed
1 year ago
0
Bug: IndexError in mcmicro and standalone
#41
josenimo
closed
1 year ago
2
Issue with cellID between nuclear and cytoplasmic masks
#40
josenimo
closed
2 years ago
3
Allow other output formats (e.g., AnnData)
#39
ArtemSokolov
opened
2 years ago
0
Enable long format for .csv output
#38
ArtemSokolov
opened
2 years ago
0
Enable post-log transform quantification
#37
ArtemSokolov
opened
2 years ago
0
Compensate for lateral spillover
#36
ArtemSokolov
opened
2 years ago
2
Robust handling of filenames with dots (`.`) in them
#35
ArtemSokolov
closed
2 years ago
0
Revert "Rewrite quantification module to allow image preprocessing before quantification"
#34
DenisSch
closed
2 years ago
0
Fixed hdf5; check for number of channels
#33
ArtemSokolov
closed
2 years ago
0
Check for a mismatch against markers.csv
#32
ArtemSokolov
closed
2 years ago
3
Rewrite quantification module to allow image preprocessing before quantification
#31
Yu-AnChen
closed
2 years ago
7
Add option to calculate custom skimage properties
#30
clemenshug
closed
3 years ago
2
Attempted fix for Issues 26 and 28 by writing CSVs to different files
#29
JoshuaHess12
closed
3 years ago
8
[Major bug] Mismatch of cells when quantifying multiple masks
#28
ArtemSokolov
closed
3 years ago
1
Add more shape features
#27
DenisSch
closed
3 years ago
0
Provide an option to move the mask suffix from column names to filenames
#26
ArtemSokolov
closed
3 years ago
1
Migrate to 1-based indexing
#25
ArtemSokolov
closed
3 years ago
1
add .btf compatibility
#24
clarenceyapp
closed
3 years ago
1
TypeError: unsupported operand type(s) for +: 'float' and 'str'
#23
DenisSch
opened
4 years ago
2
multiple mask fix spatial
#22
JoshuaHess12
closed
4 years ago
1
Multiple mask option
#21
JoshuaHess12
closed
4 years ago
3
Add spot counting
#20
DenisSch
opened
4 years ago
20
Fix accidental commit of .pyc files
#19
jmuhlich
closed
4 years ago
0
x and y coordinates are mixed up in the output
#18
ArtemSokolov
closed
4 years ago
15
check for number of csv columns to address #16
#17
JoshuaHess12
closed
4 years ago
0
If marker_name not available it throws an error
#16
DenisSch
closed
4 years ago
4
Channel name check for CyCIF structure with new CSV format
#15
JoshuaHess12
closed
4 years ago
1
Enable "minimal" and "full" CSV loading
#14
DenisSch
closed
4 years ago
3
Bug fix -- add suffix to non-unique channel names
#13
JoshuaHess12
closed
4 years ago
1
Channels with the same name handling
#12
DenisSch
closed
4 years ago
3
Remove memory usage prints
#11
DenisSch
closed
4 years ago
0
New quantification fixes memory problems #7
#10
DenisSch
closed
4 years ago
1
Error on o2
#9
DenisSch
closed
4 years ago
0
Memomory fix
#8
JoshuaHess12
closed
4 years ago
12
Memory issues
#7
DenisSch
closed
4 years ago
19
Exemplar-001 fails on 02
#6
DenisSch
closed
4 years ago
2
Included all code in the container
#5
ArtemSokolov
closed
4 years ago
0
Variable names adapted and individual file selection
#4
DenisSch
closed
4 years ago
0
Changed mask handling to single file, exact path - analogous to z-sta…
#3
JoshuaHess12
closed
4 years ago
0
Path handling fails - have you seen this before?
#2
DenisSch
closed
4 years ago
6
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