Is there a plan to include transcription foci analysis in the Starfish workflow?
No, there’s not currently.
Can you help me understand what such an analysis would look like for one of the experiments that starfish supports?
In an smFISH experiment, the transcription foci have a much higher intensity than single mRNA spots that are distributed throughout the cytoplasm. Dividing the total intensity of the transcription foci by the average single mRNA spot intensity provides an estimate of the transcription rate.
This integrated intensity measurement can be applied to other biological problems that involve large clusters of smFISH signal, e.g., mRNA in germplasm and viral particles.
The transcription foci measurement is implemented in FISH-quant, and would be a valuable implementation for Starfish, as I am not aware of anything similar written in Python.