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ImmuneDynamics / Spectre

A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
https://immunedynamics.github.io/spectre/
MIT License
56 stars 21 forks source link

Cellprofiler cannot open module #71

Closed sailseem closed 2 years ago

sailseem commented 3 years ago

Dear developer, It is a great package, but when I downloaded this package, I cannot open the project BasicSegmentation_MAC.cpproj through cellprofiler 4.2. Can you help me with that? Thanks a lot.

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tomashhurst commented 3 years ago

Hi @sailseem , hmm that's odd. Did you try opening CellProfiler first and then selecting Open --> BasicSegmentation_MAC.cpproj?

sailseem commented 3 years ago

yes, tried both, neither of them worked. Is there a compatible problem using the new MAC-version cellprofiler? Can you check that if possible? Thanks

tomashhurst commented 3 years ago

@sailseem it will probably need a new template file -- I will construct a new one, but if you need it to work in the meantime you can also download CellProfiler v3.

hrj21 commented 3 years ago

I had similar issue with the Windows pipeline. It actually told me I needed CellProfiler v4, but I only have access to v3). I just reconstructed the pipeline using your very helpful screenshots: https://wiki.centenary.org.au/display/SPECTRE/Protocol%3A+basic+cell+segmentation+using+nuclear+pixel+expansion

tomashhurst commented 3 years ago

@sailseem did you manage to get this sorted? We are hoping to do a new release during the week, and I will go back over those template files if need be. @hrj21 did your custom pipeline work OK?

hrj21 commented 3 years ago

Yes the pipeline I made in CellProfiler v3 using your screenshots seems to work perfectly well. Here's a link: https://drive.google.com/file/d/1py1kgSJ1rFtZ1wdSA6jZ1Dkp5FneGPlZ/view?usp=sharing

tomashhurst commented 3 years ago

Awesome!