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labsyspharm
/
mcmicro
Multiple-choice microscopy pipeline
https://mcmicro.org/
MIT License
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Mcmicro macsima roi
#510
josenimo
closed
1 year ago
1
Handling membrane images in Mesmer
#509
ArtemSokolov
closed
1 year ago
0
Mesmer Segmentation with a membrane channel
#508
ArozHada
closed
1 year ago
2
Add Sage-specific config
#507
adamjtaylor
closed
1 year ago
0
Windows Remote Drive Issue: Failing to create symbolic link : Operation not permitted
#506
josenimo
opened
1 year ago
2
Update s3seg to 1.5.3
#505
ArtemSokolov
closed
1 year ago
0
Update s3seg version to 1.5.2
#504
clarenceyapp
closed
1 year ago
0
mcmicro website updates
#503
hxu-hms
closed
1 year ago
0
MCMICRO compatibility with in situ sequencing
#502
rocketeer1998
opened
1 year ago
11
Input structure to run Akoya CODEX data
#501
Lucas-Maciel
opened
1 year ago
3
Create outline overlay using mesmer segmentation mask
#500
janinemelsen
opened
1 year ago
0
Update contributors and funding section of website
#499
adamjtaylor
closed
1 year ago
0
Update Cellpose container
#498
adamjtaylor
closed
1 year ago
1
background:backsub and scimap support in mcmicro
#497
JiayuanDing100
opened
1 year ago
4
Cellpose container missing ps command for NF Tower
#496
adamjtaylor
closed
1 year ago
0
Clarification of input data
#495
JiayuanDing100
closed
1 year ago
9
Consider CELESTA as a potential downstream module for MCMICRO
#494
adamjtaylor
opened
1 year ago
0
Standard pipeline for cell type annotation based on spatial feature table
#493
JiayuanDing100
closed
1 year ago
4
Rethink file tagging
#492
ArtemSokolov
opened
1 year ago
0
first pass at adding gator module to mcmicro
#491
ajitjohnson
opened
1 year ago
0
Set pyramid `downscale_factor=2` for compatibility with recyze
#490
Yu-AnChen
closed
1 year ago
1
Passing markers.csv to Auto-Minerva story construction
#489
ArtemSokolov
closed
1 year ago
0
Cleaned up and consolidated all environments under env/
#488
ArtemSokolov
closed
1 year ago
0
Added a formal devenv
#487
ArtemSokolov
closed
1 year ago
0
Modified globbing rules for mcquant's --masks
#486
ArtemSokolov
closed
1 year ago
0
minor bug: mcquant can't accept file name with no match
#485
aandytu
closed
1 year ago
3
Ilastik version bump
#484
FloWuenne
closed
1 year ago
0
How to use MCMICRO to process imaging mass cytometry (IMC) data ?
#483
sanrishiguang
opened
1 year ago
2
Kernel compatibility for singularity run
#482
ciszew
opened
1 year ago
3
Update mcmicro-ilastik container version
#481
FloWuenne
closed
1 year ago
1
Ilastik version bump
#480
ArtemSokolov
closed
1 year ago
0
Segmenting cytoplasm with S3 and Mesmer
#479
aandytu
closed
1 year ago
11
failed to pull singularity image
#478
janinemelsen
closed
1 year ago
7
Add documentation for MCMICRO on Nextflow Tower
#477
adamjtaylor
closed
1 year ago
0
Version bump for several modules
#476
ArtemSokolov
closed
1 year ago
0
quantification:mcquant error after segmentation with Mesmer
#475
nancyliy
opened
1 year ago
4
Segmentation outline with Mesmer
#474
marcovarrone
opened
1 year ago
27
Backsub update
#473
kbestak
closed
1 year ago
1
out-of-memory issue when trying to run using GPU
#472
sadhanagaddam3
closed
1 year ago
9
Backsub - updated version and documentation
#471
kbestak
closed
1 year ago
4
example output of mcmicro
#470
giovp
closed
1 year ago
2
Updated mcquant options example
#469
ArtemSokolov
closed
1 year ago
0
OSError: [Errno 28] No space left on device when trying to use mesmer with singularity
#468
rmontagn
closed
1 year ago
2
How to merge muliple tiffs into one OME.TIFF
#467
sailseem
opened
1 year ago
1
How to execute background substraction?
#466
ciszew
closed
1 year ago
8
Running Mcmicro on a non-HMS singularity HPC
#465
pakiessling
opened
1 year ago
5
Fix illumination output filename collision
#464
jmuhlich
closed
1 year ago
0
Pyramidizing the output of coreograph
#463
ArtemSokolov
closed
1 year ago
0
Update unetcoreograph version
#462
clarenceyapp
closed
1 year ago
0
Background subtraction fix
#461
kbestak
closed
1 year ago
0
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