Nucleus and cell segmentations for data in the mudRapp-seq paper

Segmentation masks for images published with the paper describing 

"Multiple direct RNA padlock probing in combination with in-situ sequencing (mudRapp-seq)":

Ahmad S, Gribling-Burrer AS, Schaust J, Fischer SC, Ambil UB, Ankenbrand MJ, Smyth RP. Visualizing the transcription and replication of influenza A viral RNAs in cells by multiple direct RNA padlock probing and in-situ sequencing (mudRapp-seq) (in review)

Raw images are published in the Bioimage Archive (identifier pending). In order to use these masks, run the data formatting code in the accompanying code repository to get the raw data in the correct structure and extract the segmentation.zip archive into analysis/segmentation.

Filenames contain a hint on how they were created:

• cp: direct segmentation with a cellpose model (nuclei, cells)
• cpws: cell segmentation through watershed with nucleus masks as seeds
• cpmc: manually corrected cellpose segmentations