Segmentation using existing coordinates

segmentation
#1

Hi,

I want to segment some split-detection AOSLO images (such as those attached), using predefined coordinates.

The goal is to analyze the size of the cells

The images are tif files.
The coordinates come from marking the center of each cell - these markings are then stored as two columns in a csv file.

Is there a way to do this using ImageJ?

Many thanks,
Emily

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#2

Hi Emily,
this sounds like seeded watershed would be well suited.
Fijji has two interactive watershed plugins (that I know of):


I don’t know if you can export seeds from a csv (or some other file format) in there though.
Maybe @iarganda would know.

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#3

Hi @Emily!

You can import them with a simple script as this one and then use the Interactive Marker-controlled Watershed plugin as suggested by @constantinpape.

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#4

Thank you @iarganda and @constantinpape for taking the time to help! Much appreciated!

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