SporeAnalyzer_1c
Analyzes hyperstacks showing bacterial spores in phase contrast and several fluorescence channels. This project is based on ImageJ in combination with ObjectJ plugin. Unlike in 'SporeTracker", spores are not followed in time.
Author: N.Vischer
Date: 4-sep 2021
Macro commands ObjectJ menu:
Analyze Spores
thresholds linked images and marks centroids with ObjectJ items type "Spore", and records mean and nearest neighbor distance
Delete Neighbors
Removes spore markers which have too close neighbors
Measure Fluor Channels
For marked spores, are circular roi is defined and the mean value in all fluorescent channels is calculated
Mark Fluor Spots chn 2
In channel 2, peaks per spore are detected by applying the maximum finder inside a circular roi. This is preceded by temporary Gaussian blur (sigma = 0.8 px). Some spores show several peaks, and thus optain several peak markers. The peak values are shown in a text column in ObjectJ results, where an entry can contain one or several space-separated values.
Mark Fluor Spots chn 3
Mark Fluor Spots chn 4
Show/Hide Circles
Displays/hides circular rois used for measuring mean fluorescence