Hello Esha -
More detail on what you did that didn’t work would be helpful.
(The best detail would be a complete, runnable script or macro
that reproduces your issue.)
How did you “segment?” Do you think your problem is with
the segmentation, or just the measurement, or both?
Are you trying to do your analysis by running commands from
the Fiji / ImageJ menu bar one by one? Or are you trying to
“automate” your analysis process by writing a script or macro?
Here is a complete, runnable IJM macro (created mostly with the
Plugins > Macros > Record...) that does
something similar to what I think you want with the “Blobs (25K)”
run("Convert to Mask");
run("Analyze Particles...", "display add in_situ");
run("Set Measurements...", "area centroid shape add redirect=None decimal=4");
(You should pretty much be able to figure out the menu commands
to run one by one, if that’s what you want, to get the same result as
running the macro.)
Here are the resulting measurements as a .csv file:
blobs_results.csv (6.5 KB)
For example, the circularity of each “particle” appears in the column
headed “Circ.” in the .csv file.
Here is the analyzed image, flattened and saved as a PNG file:
I’m not sure what you’re asking here (primarily because I’m not
sure what you actually did). Could you give more detail on what
you did, what you got, and what you wanted to get?
(As an aside, it would be helpful if instead of posting screen-shots
you could post original images, preferably in a non-lossy format
such as PNG or TIFF, rather than a lossy format such as JPEG.)