CellProfiler-plugins

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Add "Remove Edge Masks" functionality to RunCellpose plugin

1

As I was working with the RunCellpose plugin in CellProfiler, I noticed that there was a function missing that is normally available in the `IdentifyPrimaryObjects` and `IdentifySecondaryObjects` modules, which is...

jenna-tomkinson

I have added the `remove_edge_masks` function as described in #168. This will allow the user the same functionality that is provided in the `IdentifyPrimaryObjects` and `IdentifySecondaryObjects` modules (e.g. remove objects/cells/nuclei...

jenna-tomkinson

Plugins with external dependencies CAN work with binary CP distributions

2

We got plugin modules working with binary CP distributions. To do so, any dependencies can be copied out of a conda environment's `lib/site-packages` into the top-level directory of the binary....

hinerm

These three elements must all match for a plugin module to be discovered: * File name * Class name * Declared `module_name`  It seems that these items *can* be...

hinerm

Remove the direct dependency on JPype and update the yml files to be compatible with RunImageJScript

hinerm

Installation and Functionality Problems with Cellpose Plugin

2

## Installation and Functionality Problems with Cellpose Plugin: My goal is to compare Cellpose stand-alone to the Cellpose plugin inside CellProfiler But, I have run into many issues, ranging from...

jenna-tomkinson

Hi! I have been trying to run CellProfiler from source to be able to use the RunCellPose plugin. Previously, I have been able to both run CellProfiler (regular program) and...

julieaaj

Error in sys.excepthook while running cellprofiler in headless mode with CellPose as a plugin

2

[H/T the forum](https://forum.image.sc/t/error-in-sys-excepthook-while-running-cellprofiler-in-headless-mode-with-cellpose-as-a-plugin/70866). CellProfiler is running but not disengaging nicely. Can anyone verify?

bethac07

**Is your feature request related to a problem? Please describe.** Running RunCellpose with a custom model, and changing the model from the previously defined folder, doesn't warn you that the...

fefossa

TypeError in RunCellpose in GPU mode

5

Running the latest version of RunCellpose 2b3d1332e4b48fcdc12ee314421bcde5b601556a with the attached [pipeline](https://github.com/CellProfiler/CellProfiler-plugins/files/8496057/pipeline.zip) on the welcome screen example images yields the following error: ``` Traceback (most recent call last): File "C:\Users\brayma2\OneDrive -...

braymp