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CellProfiler / CellProfiler-plugins

Community-contributed and experimental CellProfiler modules.
http://plugins.cellprofiler.org/
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Contributing `ImcPluginsCP` to this repository #114

Closed votti closed 1 year ago

votti commented 3 years ago

Dear Cellprofiler team,

I would like to contribute my ImcPluginsCP plugins to CellProfiler-plugins: https://github.com/BodenmillerGroup/ImcPluginsCP

From the README: """ This repository contains CellProfiler plugins developed to facilitate working with highly multiplexed images (>40 channels).

When produced through Imaging Mass Cytometry, these images are 'intrinsically' aligned, e.g. pixels across all color planes come from the same measurement and could affect each other (e.g. channel crosstalk). To represent this, we prefer to work with mutlichannel image instead of working with individual planes (similar to 3D images that are also not analysed plane-by-plane but as a stack). This modules help Cellprofiler to better work with such stacks. """

While some of these plugins are geared towards multiplexed images, some others are also fairly generally applicable and thus may be useful for the general community. Please read the README for more information on the individual modules.

I have been maintaining these plugins publicly since 2016. The do not have any extra dependencies. I think they are fairly well documented and by-large also battle-tested. Also I tried upstream some of the chagnes to the main CP - whenever I thought that it would fit and I had time to do it.

Having these modules CellProfiler-plugins repository would simplify installation and using the modules together with the other CellProfiler-plugins. Also the visibility would increase thus maybe make it more likely that others would pick up and use the functionality of these modules.

While I wont be as actively involved in the development in the future (leaving academia by the end of the year), I still would be up for helping if there are any issues.

Please let me know what you think.

Best, Vito

ErinWeisbart commented 1 year ago

Hi Vito - Thanks for reaching out about a potential contribution. We apologize for letting this fall through the cracks initially. I see that your repo hasn't been updated in a couple years and that you were planning on leaving academia, so I'm guessing this is no longer a priority for you, but if you are still interested in having it included here, you are welcome to submit a PR with your module. To be included, it does need to be fully functional with the latest version of CellProfiler. Best - Erin