Code that is associated with the manuscript:
Epithelial Outgrowth Through Mesenchymal Rings Drives Alveologenesis
Nicholas M Negretti, Yeongseo Son, Philip Crooke, Erin J Plosa, John T Benjamin, Christopher S Jetter, Claire Bunn, Nicholas Mignemi, John Marini, Alice N Hackett, Meaghan Ransom, David Nichols, Susan H Guttentag, Heather H Pua, Timothy S Blackwell, William Zacharias, David B Frank, John A Kozub, Anita Mahadevan-Jansen, Jonathan A Kropski, Christopher V.E. Wright, Bryan Millis, Jennifer M. S. Sucre
biorxiv doi: https://doi.org/10.1101/2022.10.06.511160
Collection of scripts to process the raw data from the SOPi microscope into a useful format.
Note that the code in this repository does not generalize well and has many hardcoded settings for the microscopes used. A more generalizable analysis pipeline is currently being constructed.
Output files follow the v0.2 draft of the OME-ZARR specification.