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BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
83 stars 35 forks source link

where to download example mcd data #73

Closed sailseem closed 2 years ago

sailseem commented 3 years ago

Dear developer, That's a great pipleline for IMC analysis, but I am wondering where to download the example data- these mcd files The link below leads to a pdf pipeline only. "This pipeline was presented at the 2019 Imaging Mass Cytometry User Group Meeting. The slides can be downloaded here."

Thanks in advance.

nilseling commented 3 years ago

Hi @sailseem,

In chunk 8 of the preprocessing script, here you will download the example data. Please let me know if that works. Cheers, Nils

sailseem commented 3 years ago

Thanks, Nils, but i got an error when i run shutil.copy(file_path_csv_panel, file_path_cp_csv) FileNotFoundError: [Errno 2] No such file or directory: '../config/example_panel.csv'
I dont think it created config folder before, can you help me with that? Thanks

nilseling commented 3 years ago

The example panel file is part of this repository. Please clone the repo and setup the conda environment before you start.

sailseem commented 3 years ago

thanks, after i re-clone the repo and execute this line, the new error occurred, image

besides that, your pipeline aside that 1) Make a new pixel classification project. -> An example project that works with the example data can be found in the 'analysis' subfolder.

which I cannot find the ilastik example project under analysis. Is it because I got the error from above, can you please send me a link for downloading the example? Thanks a lot!!!

nilseling commented 3 years ago

Hey, please delete the file ../analysis/ometiff/.DS_Store. It's a Mac specific hidden file, that you can find when pressing cmd + shift + . in Finder.

Unfortunately, there is no example project available just yet - we are working on it. So please follow the instructions to set up your own project. Cheers, Nils

nilseling commented 2 years ago

I assume this resolved the issue. Please reopen if anything is unclear or open a new issue if you have more questions. Cheers, Nils