Counting cells within measured ROI

[Oceane Albert (PhD)]

Dear all,
I am new to Image J and and I am slowly starting to realize the levels of complexity it offers.
I want to measure several ROIs in my picture, and manually count cells only within those who have a minor/major axis ratio >0.85.
I tried using the freehand selection tool and measurement command, but I can't seem to link the ROIs to the measurement, select the ones that are round enough, and then link my cell count to one particular ROI.
Is there a way for me to produce a single table containing the ROI measurements and the cell count ?
Thanks a LOT for your help!
Océane

[Krs5]

Dear Océane,

You might want to have a look at BioVoxxel Toolset (http://www.biovoxxel.de/development/) ,  it includes Advanced Particle Analyzer or IJBlob + shape filter (https://code.google.com/p/ijblob) which also allows advanced filtering on shape. Both include Aspect Ratio.

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Oceane
Sent: 27 April 2016 15:19
To: [hidden email]
Subject: Counting structures within measured ROI

Dear all,
I am new to Image J and and I am slowly starting to realize the levels of complexity it offers.
I want to measure several ROIs in my picture, and manually count cells only within those who have a minor/major axis ratio >0.85.
I tried using the freehand selection tool and measurement command, but I can't seem to link the ROIs to the measurement, select the ones that are round enough, and then link my cell count to one particular ROI.
Is there a way for me to produce a single table containing the ROI measurements and the structure count ?
Thanks a LOT for your help!
Océane



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[Oceane Albert (PhD)]

Dear Kees,
thank you so much for your quick reply!
I will try that right away and report asap.
Have a great day,
Océane

[Oceane Albert (PhD)]

Dear all,
Would there been a way to filter out the ROIs based on their aspect ratio directly from the ROI manager? I cannot rely on an automatic detection of the ROIs here, so I have to contour and measure them manually anyway. I just want to preselect those in which I am going to count my cells (i.e. the round ones).
Thanks a lot,
Océane

[Olivier Burri]

Dear Oceane,

Unfortunately fitlering directly in the ROI manager the way you want is not a built-in option. What you do have left is the imageJ macro language.

You can download an example macro that does part of what you want (I do not know what you are doing for the actual measurement of your cells, but this might get you in the right track).

https://gist.github.com/lacan/73e6f82b889c4379520a11e32142aead

Best

Oli

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Oceane Albert (PhD)
Sent: mercredi, 27 avril 2016 18:53
To: [hidden email]
Subject: Re: Counting structures within measured ROI

Dear all,
Would there been a way to filter out the ROIs based on their aspect ratio directly from the ROI manager? I cannot rely on an automatic detection of the ROIs here, so I have to contour and measure them manually anyway. I just want to preselect those in which I am going to count my cells (i.e. the round ones).
Thanks a lot,
Océane



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[Oceane Albert (PhD)]

Dear Oli,
thanks so much for your help ! I will try to look into this macro which indeed looks very close to what I want to achieve.
Many many thanks,
Océane