Script to start Napari viewer

MolecularDevices Micro output consists of individual files per channel. To see multiple channels in one view, a common solution is to create and save composite images. This leads to multiplying the amount of data, and we want to avoid this if possible. Here are instructions for setting up a tool for viewing Micro data as composite images without writing them somewhere as new files:

https://github.com/UH-LMU/napari-lmu

Please note that this works only with the MolDev Micro data recorded in the Incarta style (ask Harri for details).

Once you get it working, you should see something like this:

Now you can:

• Use the Napari controls to select the channels you want to see.
• Browse to the well you are interested in.
• Save representative images.

The tool should also work with 3D, in case you have saved z-sections in Micro.

Overlay labels

The customized Napari version can also load a set of label images corresponding to the original images. The labels shown in the screenshot above represent w1 channel segmentation created with StarDist. See also an automated setup for StarDist.