pcnaDeep-napari

A customized interface for single cell track visualisation based on pcnaDeep and napari.

? Under construction

You can get test image data from pcnaDeep demo data.

TODO: usage tutorials.

Requirements

pcnaDeep
napari>=0.4.12

Usage

If you have the composite image:

# image: composite image, PCNA fluorescence the first channel, bright field the last.
# mask: PCNAdeep output binary objrct mask.
# track: PCNAdeep output tracked object table.
python launch.py --image data/MCF10A_demo_comp.tif --mask data/MCF10A_demo_mask.tif --track data/MCF10A_demo_tracks_refined.csv

Otherwise, use raw uint16 images of the above two channels with automatic pre-processing steps.

# sat: pixel saturation for rescaling PCNA and bright field.
# gamma: gamma factor for processing PCNA.
python launch.py --bf data/MCF10A_demo_bf.tif --pcna data/MCF10A_demo_pcna.tif --mask data/MCF10A_demo_mask.tif --track data/MCF10A_demo_tracks_refined.csv --sat 1 --gamma 1

This is not a napari plugin and you must launch the interface through the launch.py script.