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). 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 this zip archive into the repository root (the folder structure in the archive matches the folder structure of the repository).

Filenames in `analysis/segmentation` contain a hint about 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

Besides the final segmentation masks, the training data are included in `data/training` and the models in `models/cellpose`.

Changes:

v1.1 training data and models added