RunCellpose via docker #203
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Awesome! One comment from me
I don't think so, Docker versioning SHOULD take care of that. |
bethac07
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Jun 15, 2023
bethac07
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Jun 15, 2023
bethac07
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Jun 15, 2023
bethac07
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Jun 16, 2023
bethac07
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Aug 4, 2023
active_plugins/runcellpose.py
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| variable_revision_number = 3 | ||
| if variable_revision_number == 3: | ||
| setting_values = ["Python"] | ||
| setting_values = setting_values[0] + ["Python"] + setting_values[1:] |
DavidStirling
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Sep 25, 2023
* adding docker subprocess option to RunCellpose * Dockerfile and associated script for building RunCellpose docker * add docker documentation * better docs since docker image is automatically downloaded when requested * upgrade module version * fix upgrade settings * docs for using docker * Add model to upgrade_settings * Typo * Fix upgrade_settings fixier --------- Co-authored-by: Erin Weisbart <54687786+ErinWeisbart@users.noreply.github.com> Co-authored-by: Beth Cimini <bethac07@users.noreply.github.com> Co-authored-by: bethac07 <bcimini@broadinstitute.org>
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Here's the RunCellpose model that's been adapted to work with docker.
This version of the module allows users to use Cellpose using the .exe/.app downloaded from the CellProfiler website. All a user would have to do is download and install docker, followed by downloading the
cellprofiler/runcellpose_no_pretrainedorcellprofiler/runcellpose_with_pretraineddocker images and setting the plugins directory in CellProfiler > Preferences. These different docker images either contain or don't contain all of the Cellpose pretrained modelsOutstanding questions:
cellprofiler/runcellpose_no_pretrained:0.1andcellprofiler/runcellpose_with_pretrained:0.1are built on the pytorch CUDA docker image and as a result are pretty beefy (12GB on disk for me). Since some users may not have a CUDA GPU, it might make sense to create a slim CPU version and allow users to select this from the GUI dropdown.--gpus allhandles thisdocker_pathwork across different machines? How consistent is docker path? What is the docker path on linux?variable_revision_numberbe linked to a particular version of a docker image? Hopefully this would ensure compatibility