Using 'analyse particles' on stacks: compensating for multiple counting in adjacent slices

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Using 'analyse particles' on stacks: compensating for multiple counting in adjacent slices

Alex Lamb
Hello!


I've been using the 'analyse particles' tool on stacks, processing each slice separately. This has been working fine except that since the particles of interests are 3 dimensional they are often present in multiple neighbouring slices, so are counted multiple times.


I know that the output of the 'Stack Particle Analysis' plugin gives x,y co-ordinates of each particle identified by the tool and I was wondering if it could be possible to use these co-ordinates to discount particles that occupy the same position in adjacent slices as a way of stopping particles being counted mutliple times in neighbouring slices.


If not then is there an alternative method or plugin that will do this?


Thanks a lot!


Alex


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Re: Using 'analyse particles' on stacks: compensating for multiple counting in adjacent slices

Christine Labno-2
Hello Alex,

Have you tried 3D Objects Counter?  https://imagej.net/3D_Objects_Counter

Best,
Christine
--------------------------------------------
Christine Labno, Ph.D.
Asst. Technical Director
Light Microscopy Core
University of Chicago
Office of Shared Research Facilities
KCBD 1250 900 E. 57th St.
(773) 834-9040 (phone)

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Alex Lamb [[hidden email]]
Sent: Monday, January 08, 2018 12:36 PM
To: [hidden email]
Subject: Using 'analyse particles' on stacks: compensating for multiple counting in adjacent slices

Hello!


I've been using the 'analyse particles' tool on stacks, processing each slice separately. This has been working fine except that since the particles of interests are 3 dimensional they are often present in multiple neighbouring slices, so are counted multiple times.


I know that the output of the 'Stack Particle Analysis' plugin gives x,y co-ordinates of each particle identified by the tool and I was wondering if it could be possible to use these co-ordinates to discount particles that occupy the same position in adjacent slices as a way of stopping particles being counted mutliple times in neighbouring slices.


If not then is there an alternative method or plugin that will do this?


Thanks a lot!


Alex


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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html