Grid-wise particle counting

[Steffen Vogler]

Dear list-members,

Is there a way to run the particle counter (or any other tool that does the counting) in a grid-based manner?
The idea is the following: I have an image of a tissue section that has been stained for a certain cell marker. Since the density of cells expressing this marker is region-dependend (within one particular tissue section), I would like to generate something like a heat-map that represents the local density of cells positive for the marker of interest.
My approach would be to do multiple particle counter-runs on each single tile of a previously generated grid. Each particle-counter run should generate one spreadsheet per tile. From the final list of spreadsheets I could build the heat-map...

Again, is there a smart way to apply the particle counter sequentially on different tiles (or ROIs) in one single image?
Ideas and suggestions, how to get this implemented are more than welcome.

Thanks in advance and best regards,
Steffen      

-----
Steffen Vogler
Predoc
AG Kempermann/AG Werner

Technische Universität Dresden
DFG-Center for Regenerative Therapies Dresden
Custer of Excellence/TU Dresden
Fetscherstraße 105
01307 Dresden, Germany

t - [phone]
e - [hidden email]
Webpage: www.crt-dresden.de





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[Anderson, Charles (DNR)]

There was a previous question about turning a thresholded image into a heat map.
http://imagej.1557.n6.nabble.com/heat-map-td3690310.html

Run a mean filter of size of your local region.
Apply some LUT such as "fire"
The colour will vary depending on the mean value of the set pixels in a region
given by the filter kernel size centred at that location.

You might want to use the image showing only the particle centers if the size of the thresholded cells varies.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Steffen Vogler
Sent: Monday, July 30, 2012 9:09 AM
To: [hidden email]
Subject: Grid-wise particle counting

Dear list-members,

Is there a way to run the particle counter (or any other tool that does the counting) in a grid-based manner?
The idea is the following: I have an image of a tissue section that has been stained for a certain cell marker. Since the density of cells expressing this marker is region-dependend (within one particular tissue section), I would like to generate something like a heat-map that represents the local density of cells positive for the marker of interest.
My approach would be to do multiple particle counter-runs on each single tile of a previously generated grid. Each particle-counter run should generate one spreadsheet per tile. From the final list of spreadsheets I could build the heat-map...

Again, is there a smart way to apply the particle counter sequentially on different tiles (or ROIs) in one single image?
Ideas and suggestions, how to get this implemented are more than welcome.

Thanks in advance and best regards,
Steffen      

-----
Steffen Vogler
Predoc
AG Kempermann/AG Werner

Technische Universität Dresden
DFG-Center for Regenerative Therapies Dresden Custer of Excellence/TU Dresden Fetscherstraße 105
01307 Dresden, Germany

t - [phone]
e - [hidden email]
Webpage: www.crt-dresden.de





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