Install QuPath Instanseg extension

Open QuPath

Go to Extensions > Manage extensions

We recommend to choose "Use default", when prompted for a user directory

Install the "QuPath InstanSeg extension"

Choose the newest version and click "Install"

Open an Image

Add an annotation

Note: For running InstanSeg the very first time, we recommend using a small annotation region

Open InstanSeg extension via Extensions > InstanSeg > Run InstanSeg

The InstanSeg extension window should appear

Choose an appropriate model for your image

Choose a directory to store the model. (Only needed the first time running InstanSeg)

We recommend to "Use default"

Select channels to use for segmentation

Once all parameters are set, hit "Run"

Note: The first time InstanSeg is run, only "cpu" is available under "Prefered device". After the first time, "gpu" will also be available

The first time InstanSeg is run, you will be prompted to download PyTorch engine. Click "OK"

You might be asked multiple times. Always press "OK"

Also press "Yes" when asked to download the model

At this point it might appear like nothing is happening. Wait for ~1 min without closing the InstanSeg window. After that, the segmentation should start & appear.

After it is done, segmented cells should appear in your annotation

From now on, the option to use the gpu should be available under "Preferred device"

Using the gpu should speed up the segmentation