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Update supported_plugins.md
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sugan89 authored Dec 18, 2023
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Expand Up @@ -22,6 +22,7 @@ Those plugins that do have extra documentation contain links below.
| PixelShuffle | PixelShuffle takes the intensity of each pixel in an image and randomly shuffles its position. | No | | N/A |
| Predict | Predict allows you to use an ilastik pixel classifier to generate a probability image. CellProfiler supports two types of ilastik projects: Pixel Classification and Autocontext (2-stage). | No | | N/A |
| [RunCellpose](RunCellPose.md) | RunCellpose allows you to run Cellpose within CellProfiler. Cellpose is a generalist machine-learning algorithm for cellular segmentation and is a great starting point for segmenting non-round cells. You can use pre-trained Cellpose models or your custom model with this plugin. You can use a GPU with this module to dramatically increase your speed/efficiency. | Yes | `cellpose` | Yes |
| Runilastik | Runilasitk allows to run ilastik within CellProfiler. You can use pre-trained ilastik projects/models to predict the probability of your input images.| Yes | | Yes |
| RunImageJScript | RunImageJScript allows you to run any supported ImageJ script directly within CellProfiler. It is significantly more performant than RunImageJMacro, and is also less likely to leave behind temporary files. | Yes | `imagejscript` , though note that conda installation may be preferred, see [this link](https://py.imagej.net/en/latest/Install.html#installing-via-pip) for more information | No |
| RunOmnipose | RunOmnipose allows you to run Omnipose within CellProfiler. Omnipose is a general image segmentation tool that builds on Cellpose. | Yes | `omnipose` | No |
| RunStarDist | RunStarDist allows you to run StarDist within CellProfiler. StarDist is a machine-learning algorithm for object detection with star-convex shapes making it best suited for nuclei or round-ish cells. You can use pre-trained StarDist models or your custom model with this plugin. You can use a GPU with this module to dramatically increase your speed/efficiency. RunStarDist is generally faster than RunCellpose. | Yes | `stardist` | No |
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