TUTORIAL_python3_napari.md

PhysiCell Data Loader Tutorial: pcdl and Python and Napari

Napari is both a python library and a GUI software. Napari is used by wetlab scientists and bioinformatician to analyze fluorescent microscopy data. Napari can read ome.tiff files. https://github.com/AllenCellModeling/napari-aicsimageio

Install napari

pip3 install napari[all]

Generate ome.tiff files from the command line

pcdl_make_ome_tiff('output/')

Generate ome.tiff files from within python

import pcdl

mcdsts = pcdl.TimeSeries('output/')
mcdsts.make_ome_tiff()

Open ome.tiff files in napari from within python

import napari

viewer = napari.Viewer()
viewer.open('output/timeseries_ID.ome.tiff')

Open ome.tiff files in napari from the command line

napari output/timeseries_ID.ome.tiff

Running napari

Please work through the official documentation to learn how to run the software.

• https://napari.org/stable/tutorials/start_index.html

That's it. The rest is analysis within napari!