How SpotMAX works

SpotMAX has a highly modular architecture where each module can be run independently or sequentially.

You can also skip some of these modules or you can provide their result generated outside of SpotMAX with a separate software.

For example, you can provide the reference channel segmentation mask generated with Cellpose, skip its segmentation within SpotMAX and use it to filter valid spots (e.g., by keeping only spots that are on the reference channel mask).

The refence channel can also be used only with the intensities, e.g., to filter valid spots based on their relative intensities to the reference channel.

Note

In this section we describe how SpotMAX works not how to run it or adjust the parameters. For that, see the two sections How to run SpotMAX and Description of the parameters.

Core modules

• 1. Reference channel segmentation
  • 1.1. Image pre-processing
  • 1.2. Semantic segmentation
• 2. Spot prediction
  • 2.1. Image pre-processing
  • 2.2. Semantic segmentation
• 3. Spot detection
• 4. Spot quantification