Defining and Counting Shapes



Hi, For my lab we count rhabdomeres to quantify neurodegeneration. Rhabdomeres are the dark dots in each grouping. I circled a group of 7 rhabdomeres in blue. There are 7 in a perfect tissue sample. In a degenerated sample some of the rhabdomeres are less visible, corrupted, or not present. Can someone help create an automated or semi automated ImageJ program to quantify the number/quality of rhabdomeres per cluster, possibly by analyzing the edges. (the darkness does not relate to neurodegeneration). I also attached TIFF images depicting good quality tissue and degenerated tissue.

- marked to define rhabdomeres

- Good quality ( not degenerated) tissue

(degenerated tissue)

(another example of degenerated tissue)

I really appreciate the help.


Hi @ethanfenton -

Very cool images!!! Just to get you started a bit on your own… You can take a look at the following links to get you up-to-speed with Segmentation in ImageJ/Fiji:

The Segmentation workshop/slides will definitely help get you started with putting together a workflow for your images… And perhaps play a bit with the two suggested plugins.

Looking quickly at your images… were they all taken with the same settings on the microscope? This is necessary to create a single workflow to be applied to all images. For example - the degenerated tissue is very much over-exposed and there are no ‘objects’ that look like the image you had posted. Too - can you post the original tif of the ‘good quality’ image? For some reason… I’m only getting the RGB.