Methods and Techniques Discussion => Image Analysis => Topic started by: Lumo on January 10, 2011, 04:51:01 AM

Title: Software for counting ChAT+ rat brain cells?
Post by: Lumo on January 10, 2011, 04:51:01 AM
Hi,

We do ChAT IHC of rat brainstem. We would like to quantify the cells in a more accurate way than sitting at the microscope with a counter and some sore eyes. We are interested particularly in counting two quite small, easy identifiable strictures, the pedunculopontine and laterodorsal tegmental nuclei. I have attached an image, is there any software that could reliably count those cells? (I can take the image at higher magnification too).

I played around with a few free ones and trials but had problems with overlapping cells. We would be willing to spend only upto about 1000 on this.

Many thanks :-)
Title: Re: Software for counting ChAT+ rat brain cells?
Post by: MT Scientist on January 10, 2011, 12:54:09 PM
Have you given any thought to using fluorescence?  It might simplify the counting (bright objects)...
Title: Re: Software for counting ChAT+ rat brain cells?
Post by: Lumo on January 10, 2011, 05:22:18 PM
Unfortunately we can't do that as we don't have the correct microscope and camera.
Title: Re: Software for counting ChAT+ rat brain cells?
Post by: MT Scientist on January 11, 2011, 09:58:53 AM
While I haven't used it much, have you tried NIH Image J?  It is free for download from the NIH site.