Re: Batch Analysis and ROIset saving

Posted by Nathaniel Ryckman on Apr 13, 2011; 9:47pm
URL: http://imagej.273.s1.nabble.com/Batch-Analysis-and-ROIset-saving-tp3684918p3684923.html

Sean Burke wrote

Hello Everyone,
                    I am trying to find an easy way to do a batch analysis of 10 sets of images. Each set contains a DNA and Cytoplasmic channel. I would like to load each image, segment on the DNA Image, get the measurements for the nuclear intensity on the DNA and Cytoplasmic images, then save out the ROIset.zip with a custom or new name for the .zip file, and also save out the measurements as a csv, txt, or excel file. I am relatively new to Image J and wanted to know if anyone has any advice on this.
It would also be great if I could save out an image of the ROI mask as well.

Any help or advice would be greatly appreciated.


Sincerely,
Sean Burke

What type of cells are your cells? I got stuck with some macrophages that are heavily clumped, speckled, and unevenly lit, so I've actually been working on making a program for a couple of months. I just know someone out there has an easy way to deal with this, but, unfortunately, I can't find an easy way online.

If you have evenly lit, relatively non-clumped mammalian cells though, you should use this pipeline:

autothreshold (otsu seems popular for some reason) -> watershed -> particle analyzer -> save roi's to zip & multi-measure -> save measurements to .xls

You can use the "record macro" tool under Plugins->Macros->Record... to figure out how to do that.

Theoretically, it should take you only ~20 lines of code. Realistically, I don't think that it will happen unless you are using perfect cells.

Good luck!