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Kinetochore Analyzer

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Volker edited this page Oct 13, 2026 · 8 revisions

Segment kinetochores in yeast cells and measure the co-occurence with a molecule in a different fluorescent channel.

control image measurments

Installation

Download the file kinetochore_analyzer.ijm and put it into the macros/toolsets-folder of your FIJI installation. Restart FIJI and select the kinetochore_analyzer-toolset from the switch toolsets-button (>>).

image

Press the install or update button and follow the instructions.

Options

A right-click on a tool-button opens its options-dialog.

options
signal channel
The channel containing the signal that will be measured.
kinetochore channel
The channel containing the kinetochores.
cell channel
The channel containing the cells (can be the same as the signal channel).
cell diameter
The diameter of the cells in the image in pixel to match to the diameter of cells with which cellpose was trained.
conda path
The path to the conda environment containing your cellpose installation
model path
The path to the cellpose model
labkit classifier path
The path to the labkit classifier used to segment the kinetochores and the signal
spot label
The label representing the kinetochores or the signal in the results of the labkit classifier. If you are using the provided classifier the value is 2.
background subtraction
The intensity in each cell is subtracted from the signal before the signal is measured. The option defines which value is used for the subtraction
use gpu
If selected the cellpose model is run using the gpu. You need to have an appropriate gpu and corresponding cuda version installed. If not selected, the model is run on the cpu.
image
image file extension
The file extension of the files you want to analyze

Literature

  1. Legland, D., Arganda-Carreras, I., & Andrey, P. (2016). MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ. Bioinformatics, btw413. doi:10.1093/bioinformatics/btw413

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