SporeTrackerC

An ImageJ + ObjectJ project for analysis of spore germination

in PhC and several fluorescence channels

Norbert Vischer, 27-oct-2021

https://sils.fnwi.uva.nl/bcb/objectj/examples/sporetrackerc/MD/SporeTrackerC.html

Download SporeTrackerC and demo files

Usage:

- download the 2 demo stacks into a folder (project folder)

- download SporeTrackerC.ojj file into same project folder

- open SporeTrackerC.ojj in ImageJ with plugin ObjectJ

- Link the two demo stacks

- choose menu ObjectJ> Mark & Measure Spores

ObjectJ Menu Commands:

Mark Spores

Detects spores via maximum finder

rejects close neighbours. You kan kill invalid spores with the ObjectJ>Pistol tools

Measure Spores

measures PhC vs time

calculates germination points

measures fluorescence vs time (channels >=2)

creates plot family PhC

creates plot family fluorescence

creates montage

stores montage and plot families in Aux folder

Note: fluorescence values are the mean value

of a circle with radius fluorRad = 10 px, minus background

Re-load Plots and Montages (Aux)

Re-loads plots and motages from the Aux folder (which is located in the projects folder)

Re-create Plots and Montages

Using spore markers in frame 1, chn1, fluorescence

values, plots and montages are recalculated

and stores montage and plot families in Aux folder

Make Super-imposed Fluor Plots

For each channel, a plot is created with all fluorescence lines being superimposed.

You are asked to synchronize the plots by defining germination time = 0.

Show Previous Object [1]

Show Next Object 2]

Show Selected Object [3]

Show Object # ...[4]

Shows the related slices in plot families and montage

and the related object the original linked image.

Note: if you kill or add objects (=spore markers),

you need to re-create montages and plot families

Output Table

Shows a table containing time, phase and fluorescence data

of all spores.

Toggle Qualification

If an object is selected (e.g. in ObjectJ Results, or in the image via the ObjectJ Finger tool),

its qualification flag is inverted. Non-qulaified objects have gray number labels in braces.

Clean Plots and Montages

Checks if Plots or montages contain data from deleted objects, and cleans them if

necessary. For this, the negative ID numbers in the label field are checked for validity.