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Updated documentation
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sugan89 committed Feb 6, 2024
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Expand Up @@ -21,3 +21,4 @@ Information about select plugins is as follows:

**ClassifyPixelsUNET**: ClassifyPixelsUNET is a pixel classifier for background/object edge/object body. As far as we are aware, other deep learning based plugins that we do currently support (such as RunCellpose) work better.
**DeclumpObjects**: DeclumpObjects will split objects based on a seeded watershed method. Functionality from this module was [added into CellProfiler](https://github.com/CellProfiler/CellProfiler/pull/4397) in the Watershed module as of CellProfiler 4.2.0.
**Predict**: Predict module is not supported anymore and one can use **Runilastik** module to run ilastik pixel classifier in Cellprofiler.
4 changes: 2 additions & 2 deletions documentation/CP-plugins-documentation/using_plugins.md
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Expand Up @@ -21,7 +21,7 @@ See [Installing plugins with dependencies, using CellProfiler from source](#inst
See [Installing plugins with dependencies, using pre-built CellProfiler](#installing-plugins-with-dependencies-using-pre-built-cellprofiler).
- The third option uses Docker to bypass installation requirements.
It is the simplest option that only requires download of Docker Desktop; the module that has dependencies will automatically download a Docker that has all of the dependencies upon run and access that Docker while running the plugin.
It is currently only supported for the RunCellpose plugin but will be available in other plugins soon.
It is currently supported for the RunCellpose and Runilastik plugins. Please have a look at this [table](https://github.com/CellProfiler/CellProfiler-plugins/blob/master/documentation/CP-plugins-documentation/supported_plugins.md) to know about the availability of docker versions for plugins.
See [Using Docker to Bypass Installation Requirements](#using-docker-to-bypass-installation-requirements).

### Installing plugins without dependencies
Expand Down Expand Up @@ -173,7 +173,7 @@ Download Docker Desktop from [Docker.com](https://www.docker.com/products/docker

2. **Run Docker Desktop**
Open Docker Desktop.
Docker Desktop will need to be open every time you use a plugin with Docker.
Docker Desktop will need to be open every time you use a plugin with Docker. Please have a look at this [table](https://github.com/CellProfiler/CellProfiler-plugins/blob/master/documentation/CP-plugins-documentation/supported_plugins.md) to know if a docker version is available for a plugin.

3. **Select "Run with Docker"**
In your plugin, select `Docker` for "Run module in docker or local python environment" setting.
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