mm-plugin

Plug-in guidance for developing MicroManager plugins can be found here.

Getting Started

If you're running on linux you need to build the source code to install micromanager. If you're running on macOS or Windows you can use the prebuilt binaries.

Install a More Current Version of MicroManager

Building the Source (Linux)

You can build source code using the provided Dockerfile. This build is the ImageJ plugin version of Micro-Manager.

docker build -f ./docker/Dockerfile.mm -t mm-ij .

If you run the image, it will copy ImageJ and the plugin to the /dest directory. If you mount a local directory to /dest, it will copy the files there.

mkdir -p mm_install
docker run --rm -v $(pwd)/mm_install:/dest mm-ij

Windows

The prebuilt binaries for Windows can be downloaded from the releases page

mkdir -p mm_install
curl -o mm_install/MMSetup.exe https://download.micro-manager.org/nightly/2.0/Windows/MMSetup_64bit_2.0.3_20250629.exe
.\mm_install\MMSetup.exe

You may need to restart the computer after installation.

Get the MicroManager Source Code

Run the following command to get the micromanager source code in the micro-manager directory:

git submodule update --init --recursive

This book is helpful for writing plugins

https://imagingbook.com https://link.springer.com/book/10.1007/978-3-031-05744-1, Appendix I

Developing

The plugin code is in the flfm directory.

To check formatting, run

cd flfm
mvn spotless:check

To format the code, run

cd flfm
mvn spotless:apply

Models need to go into src/main/resources/models they should be named according the number of iters they perform. For example, model_1.pt will come up in the dropdown as 1.

To ensure that the GPU can be seen when running from ImageJ, start with the following code snippet:

./ImageJ -cp ./plugins/flfm_plugin.jar

Docker Development:

Make sure to have the NVIDIA Container Toolkit is installed

Configure the Container toolkit.

Build the docker image:

docker build --tag=mm:latest -f ./docker/Dockerfile.mm .

Can run the docker image with x11docker

x11docker --desktop --user=RETAIN --verbose mm:latest