Re: Batch Analysis and ROIset saving

Posted by Nathaniel Ryckman on Apr 13, 2011; 9:49pm
URL: http://imagej.273.s1.nabble.com/Batch-Analysis-and-ROIset-saving-tp3684918p3684919.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

By the way, if you do not have experience programming, you might also want to give cell profiler a try. Some scientists also settle for that software. The reason that I mention CellProfiler is that you can also use imageJ through CellProfiler for specialized tasks.

I tried CellProfiler, and it wasn't very customizable. I would only use it if you are interested in "relative quality" (aka assuming your control population has about as much error as your variable population).