Hello Rico.

It is not so difficult to count cells in tissue slices.

You could double-label the cells of interest with a specific cellular marker and DAPI. What you definitely need is a fluorescence microscope. You are working at a large university. I can hardly imagine that there is no scientific group with such a microscope. There may be even a core imaging facility available (f.e. the Bakewell NeuroImaging Laboratory). You have to broaden your network at your university and contact those groups. It is worth asking, they wan´t cut your head off ;-). Microscopes are very expensive.

If you have taken the images - I think 20x magnification would be sufficient, you can use several methods for counting nuclei via ImageJ (a java-based free software):

- manually: with the CellCounter PlugIn

- semiautomatically: with the ParticleCounting PlugIn

Here are some links:

- Blakewell NeuroImaging Laboratory: http://thalamus.wustl.edu/Facilities/Bakewell

- ImageJ: http://imagej.nih.gov/ij/

- ImageJ download with a lot of PlugIns uncluded: http://www.uhnresearch.ca/facilities/wcif/imagej/installing_imagej.htm

- ImageJ Wiki: http://imagejdocu.tudor.lu/

- Particle counting with ImageJ: http://imagejdocu.tudor.lu/doku.php?id=video:analysis:particle_counting_-_automated_and_manual

Hope this helps!

When you mention cheapest microscope set-up I was wondering about how you would actually wanted to count the neurons. Maybe there are ways to count neurons just using microscope and entering numbers  manually. What I know of counting of neurons on section can be best and fastest without bias and error can be perform by using Stereological software (interface with camera and computer). It is expensive but you can always ready with your stained sections (DAB stained sections prefered) and approach to those labs having stereology software. 

Hello Rico.

It is not so difficult to count cells in tissue slices.

You could double-label the cells of interest with a specific cellular marker and DAPI. What you definitely need is a fluorescence microscope. You are working at a large university. I can hardly imagine that there is no scientific group with such a microscope. There may be even a core imaging facility available (f.e. the Bakewell NeuroImaging Laboratory). You have to broaden your network at your university and contact those groups. It is worth asking, they wan´t cut your head off ;-). Microscopes are very expensive.

If you have taken the images - I think 20x magnification would be sufficient, you can use several methods for counting nuclei via ImageJ (a java-based free software):

- manually: with the CellCounter PlugIn

- semiautomatically: with the ParticleCounting PlugIn

Here are some links:

- Blakewell NeuroImaging Laboratory: http://thalamus.wustl.edu/Facilities/Bakewell

- ImageJ: http://imagej.nih.gov/ij/

- ImageJ download with a lot of PlugIns uncluded: http://www.uhnresearch.ca/facilities/wcif/imagej/installing_imagej.htm

- ImageJ Wiki: http://imagejdocu.tudor.lu/

- Particle counting with ImageJ: http://imagejdocu.tudor.lu/doku.php?id=video:analysis:particle_counting_-_automated_and_manual

Hope this helps!