FFU COVID
收藏资源简介：
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.
