FFU COVID

Fiji/ImageJ macro code to analyse focus forming unit assays in Vero cells infected with COVID-19. Macro was developed by Cameron J Nowell of Monash University (cameron.nowell@monash.edu) in collaboration with Ben Croker (bcroker@uscd.edu)

Code will take ND2 files captured on a Nikon microscope and analyse the following parameters from an fluorescent FFU assay

- Positive cell number

- Postive cluster area

- Positive cluster cell density

- Positive cluster staining intensity

- Positive cluster shape as a ratio of perimeter to convex hull ratio

- Positive cluster distance from edge and other clusters

Requirements to run

- Standard install of the Fiji distribution of ImageJ (www.fiji.sc)

- Morphology Plugins by Gabriel Landini

- StartDist DeepLearning Segmentation

- CSDeep plugin for running CARE networks

- Clij and Clij2 GPU accelrated filtering plugins

- NND calculation plugin from Yuxiong Mao (https://icme.hpc.msstate.edu/mediawiki/index.php/Nearest_Neighbor_Distances_Calculation_with_ImageJ.html)

- Ilastik machine learing package (https://ilastik.org/)

Assumptions

- Data is captured with two channels (Ch1=nuclei, Ch2=positive marker) and saved in Nikon ND2 format

- Each well is captured as a single field or stiched highpower fields to show the whole well.

Code is able to work with multiple wells in a plate

Demo data for two wells and an ilatik project file are linked to be able to test run the code.