RNAScope data compatible?

[KunHHE]

Hi @ctcisar, thanks you for developing such cool tool. May I ask if this extsion of starfish is compatible with RNAScope data? Thank you!

[ctcisar]

Hello!
Reading through the promotional materials for RNAScope, it does appear to be an experiment type that should be compatible with PIPEFISH. That said, we were not able to get our hands on an example dataset to test whether it works with PIPEFISH.

Given our experience with other ISH experiments, compatibility depends entirely on whether the machine provides high-resolution images from the hybridization rounds and the encoding used for the codebook or not. Many tools exclusively provide low-resolution hybridization images, which are not sufficient to validate the decoding with PIPEFISH.

Best,
Cecilia Cisar