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(part 1) Step 5: average BB shape quantification

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Eugene Katrukha edited this page Mar 14, 2025 · 2 revisions

In the final step of this part, again, make sure that the Correlescence plugin version >= 0.0.7 is installed on your FIJI.

At this step quantification of the shape of the averaged BB (total protein stain channel) is performed.

Open FIJI and run s3c_estimate_diam.ijm macro.
The parameters are the same as in other macros.

Select a folder where the average volume (per cell) tif file is stored.

output

The macro creates a csv file with the same name as tif, containing
diameter and XY center coordinates of the BB (total protein channel).

what happens

Each slice of the final average image is fitted to the concentric circles template
in the same way as it is described in step 1.

Developed in Cell Biology group of Utrecht University.
The plugin and this wiki are under constant development.
E-mail for any questions, feedback, errors or suggestion or tag @ekatrukha at image.sc forum.

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