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

#50 - Issue Generating the analysis stacks

Issue - State: closed - Opened by aleixriusr about 4 years ago - 3 comments

#50 - Issue Generating the analysis stacks

Issue - State: closed - Opened by aleixriusr about 4 years ago - 3 comments

#49 - Pipeline not compatible with CellProfiler V4

Issue - State: closed - Opened by jobha about 4 years ago - 4 comments

#49 - Pipeline not compatible with CellProfiler V4

Issue - State: closed - Opened by jobha about 4 years ago - 4 comments

#48 - How to generate .txt files form acquisition of .mcd files?

Issue - State: closed - Opened by KaWingLee9 about 4 years ago - 2 comments

#48 - How to generate .txt files form acquisition of .mcd files?

Issue - State: closed - Opened by KaWingLee9 about 4 years ago - 2 comments

#47 - How

Issue - State: closed - Opened by KaWingLee9 about 4 years ago

#47 - How

Issue - State: closed - Opened by KaWingLee9 about 4 years ago

#46 - Error loading zipped mcd/txt file

Issue - State: closed - Opened by Bunmi0616 about 4 years ago - 8 comments

#46 - Error loading zipped mcd/txt file

Issue - State: closed - Opened by Bunmi0616 about 4 years ago - 8 comments

#45 - Error in generating ome.tiff from mcd

Issue - State: closed - Opened by hfl112 over 4 years ago - 3 comments

#45 - Error in generating ome.tiff from mcd

Issue - State: closed - Opened by hfl112 over 4 years ago - 3 comments

#44 - Memory issue in CellProfiler when running Measure_mask pipeline

Issue - State: closed - Opened by cjauset over 4 years ago - 1 comment

#44 - Memory issue in CellProfiler when running Measure_mask pipeline

Issue - State: closed - Opened by cjauset over 4 years ago - 1 comment

#43 - Problem Generating Analysis Stack Tiffs

Issue - State: closed - Opened by cassandraman over 4 years ago - 9 comments

#43 - Problem Generating Analysis Stack Tiffs

Issue - State: closed - Opened by cassandraman over 4 years ago - 9 comments

#42 - Error converting mcd containing folders into imc zip folders

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

#42 - Error converting mcd containing folders into imc zip folders

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

#41 - How to adapt the pipeline for 'tissue level' maks

Issue - State: closed - Opened by votti over 4 years ago - 10 comments

#41 - How to adapt the pipeline for 'tissue level' maks

Issue - State: closed - Opened by votti over 4 years ago - 10 comments

#40 - Index Error in 3_measure_mask.cppipe

Issue - State: closed - Opened by hfl112 over 4 years ago - 4 comments

#40 - Index Error in 3_measure_mask.cppipe

Issue - State: closed - Opened by hfl112 over 4 years ago - 4 comments

#39 - Error with load zip file

Issue - State: closed - Opened by hfl112 over 4 years ago - 2 comments

#39 - Error with load zip file

Issue - State: closed - Opened by hfl112 over 4 years ago - 2 comments

#38 - [WIP] Implement Pipeline as Snakemake workflow

Pull Request - State: closed - Opened by votti over 4 years ago - 1 comment

#38 - [WIP] Implement Pipeline as Snakemake workflow

Pull Request - State: closed - Opened by votti over 4 years ago - 1 comment

#37 - Citation

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

#37 - Citation

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

#36 - ilastik project

Issue - State: closed - Opened by SchulzDan over 4 years ago - 1 comment

#36 - ilastik project

Issue - State: closed - Opened by SchulzDan over 4 years ago - 1 comment

#35 - Fixes the imctoools version to v1.0.7

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

#35 - Fixes the imctoools version to v1.0.7

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

#34 - Added link to UGM slides in README.md

Pull Request - State: closed - Opened by ndamond over 4 years ago

#34 - Added link to UGM slides in README.md

Pull Request - State: closed - Opened by ndamond over 4 years ago

#33 - Issue converting mcd containing folders into imc zip folders

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

#33 - Issue converting mcd containing folders into imc zip folders

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

#32 - Issue running 1_prepare_ilastik_edit

Issue - State: closed - Opened by bitttyyyy almost 5 years ago - 2 comments

#32 - Issue running 1_prepare_ilastik_edit

Issue - State: closed - Opened by bitttyyyy almost 5 years ago - 2 comments

#31 - histocat doesn't open output histocat file

Issue - State: closed - Opened by minhtran1309 almost 5 years ago - 2 comments

#31 - histocat doesn't open output histocat file

Issue - State: closed - Opened by minhtran1309 almost 5 years ago - 2 comments

#30 - Additional instructions to make pipeline work

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

#30 - Additional instructions to make pipeline work

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

#29 - ImportError: DLL load failed: The specified module could not be found.

Issue - State: closed - Opened by cw739 about 5 years ago - 1 comment

#29 - ImportError: DLL load failed: The specified module could not be found.

Issue - State: closed - Opened by cw739 about 5 years ago - 1 comment

#27 - Jupyter notebook won't launch

Issue - State: closed - Opened by sarahjconley about 5 years ago - 11 comments

#27 - Jupyter notebook won't launch

Issue - State: closed - Opened by sarahjconley about 5 years ago - 11 comments

#26 - `probability2uncertainty` script `cannot compress LZW`

Issue - State: closed - Opened by votti about 5 years ago

#26 - `probability2uncertainty` script `cannot compress LZW`

Issue - State: closed - Opened by votti about 5 years ago

#25 - CellProfiler "Load Pipeline" Error

Issue - State: closed - Opened by juliannehoeflich about 5 years ago - 2 comments

#25 - CellProfiler "Load Pipeline" Error

Issue - State: closed - Opened by juliannehoeflich about 5 years ago - 2 comments

#24 - basic question: how to add imctools to conda using a PC

Issue - State: closed - Opened by blueequinox about 5 years ago - 1 comment

#24 - basic question: how to add imctools to conda using a PC

Issue - State: closed - Opened by blueequinox about 5 years ago - 1 comment

#23 - Export cell outline as .tiff

Pull Request - State: closed - Opened by toobiwankenobi over 5 years ago - 2 comments

#23 - Export cell outline as .tiff

Pull Request - State: closed - Opened by toobiwankenobi over 5 years ago - 2 comments

#22 - Export cell outline as .tiff image

Pull Request - State: closed - Opened by toobiwankenobi over 5 years ago

#22 - Export cell outline as .tiff image

Pull Request - State: closed - Opened by toobiwankenobi over 5 years ago

#21 - Cell Outline Export

Pull Request - State: closed - Opened by toobiwankenobi over 5 years ago - 1 comment

#21 - Cell Outline Export

Pull Request - State: closed - Opened by toobiwankenobi over 5 years ago - 1 comment

#20 - Histocat Inquiry

Issue - State: closed - Opened by juliannehoeflich over 5 years ago - 3 comments

#20 - Histocat Inquiry

Issue - State: closed - Opened by juliannehoeflich over 5 years ago - 3 comments

#19 - Error in generating the histocat folder with masks

Issue - State: closed - Opened by cassandraman over 5 years ago - 3 comments

#19 - Error in generating the histocat folder with masks

Issue - State: closed - Opened by cassandraman over 5 years ago - 3 comments

#18 - zipfile error

Issue - State: closed - Opened by al-khalidi over 5 years ago - 3 comments

#18 - zipfile error

Issue - State: closed - Opened by al-khalidi over 5 years ago - 3 comments

#17 - Github does not render ipynb

Issue - State: closed - Opened by votti over 5 years ago - 1 comment

#17 - Github does not render ipynb

Issue - State: closed - Opened by votti over 5 years ago - 1 comment

#16 - Running everything fully automated

Issue - State: closed - Opened by votti over 5 years ago - 2 comments

#16 - Running everything fully automated

Issue - State: closed - Opened by votti over 5 years ago - 2 comments

#15 - Add a `How to adapt workflow to new data` section

Issue - State: closed - Opened by votti over 5 years ago - 2 comments
Labels: enhancement

#15 - Add a `How to adapt workflow to new data` section

Issue - State: closed - Opened by votti over 5 years ago - 2 comments
Labels: enhancement

#14 - Add a well trained example ilastik classifier to the example data

Issue - State: closed - Opened by votti over 5 years ago - 1 comment
Labels: enhancement

#14 - Add a well trained example ilastik classifier to the example data

Issue - State: closed - Opened by votti over 5 years ago - 1 comment
Labels: enhancement

#13 - comments on readme and example run through

Issue - State: closed - Opened by glynnelson over 5 years ago - 7 comments

#13 - comments on readme and example run through

Issue - State: closed - Opened by glynnelson over 5 years ago - 7 comments

#12 - example data

Issue - State: closed - Opened by goodforthebrain over 5 years ago - 8 comments
Labels: question

#12 - example data

Issue - State: closed - Opened by goodforthebrain over 5 years ago - 8 comments
Labels: question

#11 - Script: Rename Input folders -> Configurations

Issue - State: closed - Opened by votti over 5 years ago

#11 - Script: Rename Input folders -> Configurations

Issue - State: closed - Opened by votti over 5 years ago

#10 - Wrong command to start notebook

Issue - State: closed - Opened by votti over 5 years ago

#10 - Wrong command to start notebook

Issue - State: closed - Opened by votti over 5 years ago

#8 - Looking for 201805_cp_segmentation_example imc_full_sm.tiff

Issue - State: closed - Opened by arcolombo almost 6 years ago - 3 comments

#7 - NaNs not allowed with masked objects

Issue - State: closed - Opened by razaalipath almost 6 years ago

#6 - Moving the configurations in a configuration file

Issue - State: closed - Opened by votti almost 6 years ago - 1 comment

#5 - Better error handling

Issue - State: open - Opened by votti almost 6 years ago - 5 comments

#4 - Conda doesnt install imctools in Mac

Issue - State: closed - Opened by Rcasan about 6 years ago - 5 comments

#3 - Jupyter notebook error: no module named 'imctools'

Issue - State: closed - Opened by SteveBoothHLI about 6 years ago - 5 comments

#2 - Error Processing imctools in Conda

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

#1 - Question about H5 output in the imcSegmentation Pipeline

Issue - State: closed - Opened by arcolombo over 6 years ago - 4 comments