Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / bodenmillergroup/imcsegmentationpipeline issues and pull requests

#101 - Errors setting up with example data

Issue - State: closed - Opened by honeybee-224 over 2 years ago - 3 comments

#101 - Errors setting up with example data

Issue - State: closed - Opened by honeybee-224 over 2 years ago - 3 comments

#100 - imwrite() got an unexpected keyword argument 'compress'

Issue - State: closed - Opened by ingros over 2 years ago - 9 comments

#100 - imwrite() got an unexpected keyword argument 'compress'

Issue - State: closed - Opened by ingros over 2 years ago - 9 comments

#99 - Remove tifffile pinning

Pull Request - State: closed - Opened by jwindhager over 2 years ago

#99 - Remove tifffile pinning

Pull Request - State: closed - Opened by jwindhager over 2 years ago

#98 - Select ROIs for analysis

Issue - State: closed - Opened by Jeffchingg over 2 years ago - 2 comments

#98 - Select ROIs for analysis

Issue - State: closed - Opened by Jeffchingg over 2 years ago - 2 comments

#97 - SummarizeStack module cannot be loaded properly

Issue - State: closed - Opened by Jeffchingg over 2 years ago - 3 comments

#97 - SummarizeStack module cannot be loaded properly

Issue - State: closed - Opened by Jeffchingg over 2 years ago - 3 comments

#96 - BadZipFile error

Issue - State: closed - Opened by Jeffchingg over 2 years ago - 2 comments

#96 - BadZipFile error

Issue - State: closed - Opened by Jeffchingg over 2 years ago - 2 comments

#95 - '{sys.executable}' is not recognized; imcsegpipe not found

Issue - State: closed - Opened by Jeffchingg over 2 years ago - 8 comments

#95 - '{sys.executable}' is not recognized; imcsegpipe not found

Issue - State: closed - Opened by Jeffchingg over 2 years ago - 8 comments

#94 - Corrupt MCD

Issue - State: closed - Opened by Laner over 2 years ago - 8 comments

#94 - Corrupt MCD

Issue - State: closed - Opened by Laner over 2 years ago - 8 comments

#92 - Unexpected argument 'compress'

Issue - State: closed - Opened by Laner over 2 years ago - 2 comments
Labels: duplicate

#92 - Unexpected argument 'compress'

Issue - State: closed - Opened by Laner over 2 years ago - 2 comments
Labels: duplicate

#91 - Hotfix xtiff/tifffile issue

Pull Request - State: closed - Opened by jwindhager over 2 years ago
Labels: bug

#91 - Hotfix xtiff/tifffile issue

Pull Request - State: closed - Opened by jwindhager over 2 years ago
Labels: bug

#90 - write() got an unexpected keyword argument 'compress'

Issue - State: closed - Opened by olivierbortolotti over 2 years ago - 4 comments

#90 - write() got an unexpected keyword argument 'compress'

Issue - State: closed - Opened by olivierbortolotti over 2 years ago - 4 comments

#89 - sort analysis stack channels by mass (closes #88)

Pull Request - State: closed - Opened by jwindhager over 2 years ago - 2 comments
Labels: enhancement

#89 - sort analysis stack channels by mass (closes #88)

Pull Request - State: closed - Opened by jwindhager over 2 years ago - 2 comments
Labels: enhancement

#88 - Channel order in pre-trained ilastik classifier

Issue - State: closed - Opened by nilseling over 2 years ago - 3 comments
Labels: enhancement

#88 - Channel order in pre-trained ilastik classifier

Issue - State: closed - Opened by nilseling over 2 years ago - 3 comments
Labels: enhancement

#87 - v3

Pull Request - State: closed - Opened by jwindhager over 2 years ago - 6 comments

#87 - v3

Pull Request - State: closed - Opened by jwindhager over 2 years ago - 6 comments

#86 - Addition of documentation and adjustment to pipeline

Pull Request - State: closed - Opened by nilseling over 2 years ago

#86 - Addition of documentation and adjustment to pipeline

Pull Request - State: closed - Opened by nilseling over 2 years ago

#85 - v3

Pull Request - State: closed - Opened by jwindhager almost 3 years ago - 13 comments

#85 - v3

Pull Request - State: closed - Opened by jwindhager almost 3 years ago - 13 comments

#84 - p values for neighborhood analysis

Issue - State: closed - Opened by Bunmi0616 almost 3 years ago - 3 comments

#84 - p values for neighborhood analysis

Issue - State: closed - Opened by Bunmi0616 almost 3 years ago - 3 comments

#83 - First steps in Jupyter for MCD pre-processing?

Issue - State: closed - Opened by DOCroit almost 3 years ago - 2 comments

#83 - First steps in Jupyter for MCD pre-processing?

Issue - State: closed - Opened by DOCroit almost 3 years ago - 2 comments

#82 - Add deprecation note

Pull Request - State: closed - Opened by votti about 3 years ago - 4 comments

#82 - Add deprecation note

Pull Request - State: closed - Opened by votti about 3 years ago - 4 comments

#81 - No session JSON files available

Issue - State: closed - Opened by edtruelove1 about 3 years ago - 2 comments

#81 - No session JSON files available

Issue - State: closed - Opened by edtruelove1 about 3 years ago - 2 comments

#80 - How to perform the analysis without histocat?

Issue - State: closed - Opened by luglilab about 3 years ago - 2 comments

#80 - How to perform the analysis without histocat?

Issue - State: closed - Opened by luglilab about 3 years ago - 2 comments

#79 - Assertion Error in imc_preprocessing

Issue - State: closed - Opened by marinabroz about 3 years ago - 3 comments

#79 - Assertion Error in imc_preprocessing

Issue - State: closed - Opened by marinabroz about 3 years ago - 3 comments

#78 - Fluorescence image analysis?!?!

Issue - State: closed - Opened by sittnerr about 3 years ago - 1 comment

#78 - Fluorescence image analysis?!?!

Issue - State: closed - Opened by sittnerr about 3 years ago - 1 comment

#77 - setup problem

Issue - State: closed - Opened by sittnerr about 3 years ago - 8 comments

#77 - setup problem

Issue - State: closed - Opened by sittnerr about 3 years ago - 8 comments

#76 - ilastik classification

Issue - State: closed - Opened by sailseem about 3 years ago - 2 comments

#76 - ilastik classification

Issue - State: closed - Opened by sailseem about 3 years ago - 2 comments

#75 - error in 1_prepare_ilastik

Issue - State: closed - Opened by simeonmayala about 3 years ago - 1 comment

#75 - error in 1_prepare_ilastik

Issue - State: closed - Opened by simeonmayala about 3 years ago - 1 comment

#74 - Error while running IMCtools

Issue - State: closed - Opened by raman91 about 3 years ago - 1 comment

#74 - Error while running IMCtools

Issue - State: closed - Opened by raman91 about 3 years ago - 1 comment

#73 - where to download example mcd data

Issue - State: closed - Opened by sailseem about 3 years ago - 6 comments

#73 - where to download example mcd data

Issue - State: closed - Opened by sailseem about 3 years ago - 6 comments

#72 - Export Scaling_FullStackFiltered

Issue - State: closed - Opened by nilseling over 3 years ago - 4 comments

#72 - Export Scaling_FullStackFiltered

Issue - State: closed - Opened by nilseling over 3 years ago - 4 comments

#71 - Generation of histocat folders with mask

Issue - State: closed - Opened by veenstje over 3 years ago - 3 comments

#71 - Generation of histocat folders with mask

Issue - State: closed - Opened by veenstje over 3 years ago - 3 comments

#70 - Removed all quotation marks from pipelines

Pull Request - State: closed - Opened by nilseling over 3 years ago - 1 comment

#70 - Removed all quotation marks from pipelines

Pull Request - State: closed - Opened by nilseling over 3 years ago - 1 comment

#69 - Error in initial pipeline with example data

Issue - State: closed - Opened by veenstje over 3 years ago - 4 comments

#69 - Error in initial pipeline with example data

Issue - State: closed - Opened by veenstje over 3 years ago - 4 comments

#67 - implementation of mcd file checks

Issue - State: closed - Opened by SchulzDan over 3 years ago - 2 comments

#67 - implementation of mcd file checks

Issue - State: closed - Opened by SchulzDan over 3 years ago - 2 comments

#65 - Fix image rescaling bug

Pull Request - State: closed - Opened by votti over 3 years ago - 1 comment

#65 - Fix image rescaling bug

Pull Request - State: closed - Opened by votti over 3 years ago - 1 comment

#64 - CP4 pipeline error

Issue - State: closed - Opened by SchulzDan over 3 years ago - 1 comment

#64 - CP4 pipeline error

Issue - State: closed - Opened by SchulzDan over 3 years ago - 1 comment

#63 - Panel import with manually opened channels

Issue - State: closed - Opened by lecords over 3 years ago - 4 comments

#63 - Panel import with manually opened channels

Issue - State: closed - Opened by lecords over 3 years ago - 4 comments

#62 - Key Error when using own data

Issue - State: closed - Opened by hannahetompkins over 3 years ago - 13 comments

#62 - Key Error when using own data

Issue - State: closed - Opened by hannahetompkins over 3 years ago - 13 comments

#61 - Move spillover matrix and panel to example data

Issue - State: closed - Opened by nilseling almost 4 years ago - 1 comment

#61 - Move spillover matrix and panel to example data

Issue - State: closed - Opened by nilseling almost 4 years ago - 1 comment

#60 - no session JSON files available.

Issue - State: closed - Opened by rachel662 almost 4 years ago - 1 comment

#60 - no session JSON files available.

Issue - State: closed - Opened by rachel662 almost 4 years ago - 1 comment

#59 - Truncates image range to 0-1 for mean image in 1_prepare_ilastik

Pull Request - State: closed - Opened by votti almost 4 years ago - 5 comments

#59 - Truncates image range to 0-1 for mean image in 1_prepare_ilastik

Pull Request - State: closed - Opened by votti almost 4 years ago - 5 comments

#58 - Update 3_measure_mask_basic.cppipe

Pull Request - State: closed - Opened by PierreBSC almost 4 years ago - 8 comments

#58 - Update 3_measure_mask_basic.cppipe

Pull Request - State: closed - Opened by PierreBSC almost 4 years ago - 8 comments

#57 - Images of type float must be between -1 and 1

Issue - State: closed - Opened by StarXian almost 4 years ago - 3 comments

#57 - Images of type float must be between -1 and 1

Issue - State: closed - Opened by StarXian almost 4 years ago - 3 comments

#56 - Computation of cell morphological features

Issue - State: closed - Opened by PierreBSC almost 4 years ago - 7 comments

#56 - Computation of cell morphological features

Issue - State: closed - Opened by PierreBSC almost 4 years ago - 7 comments

#55 - Ilastik error 'failed to generate export files'

Issue - State: closed - Opened by rachel662 almost 4 years ago - 6 comments

#55 - Ilastik error 'failed to generate export files'

Issue - State: closed - Opened by rachel662 almost 4 years ago - 6 comments

#54 - Dimesion mismatch between 'masks' & 'image'-tiffs after 2_segment_ilastik

Issue - State: closed - Opened by maxgrigori almost 4 years ago - 7 comments

#54 - Dimesion mismatch between 'masks' & 'image'-tiffs after 2_segment_ilastik

Issue - State: closed - Opened by maxgrigori almost 4 years ago - 7 comments

#53 - Updates the example pipeline outline to CP4 and imctools v2

Pull Request - State: closed - Opened by votti almost 4 years ago

#53 - Updates the example pipeline outline to CP4 and imctools v2

Pull Request - State: closed - Opened by votti almost 4 years ago

#51 - Add output folder to save filtered and compensated tiff files

Issue - State: closed - Opened by nilseling about 4 years ago - 1 comment

#51 - Add output folder to save filtered and compensated tiff files

Issue - State: closed - Opened by nilseling about 4 years ago - 1 comment