We are attempting to develop a protocol for cryostat section on adult male and female mice brains. I was curious to see if anyone had a protocol that listed approximately how deep into the brain (starting in the forebrain) you may need to cut before reaching the beginning of the hippocampus.
The slices are smaller from mice and so the experimenter has to have "good hands" and practice with dealing smaller brain. By using the vibratome control we used to start cutting (Ventral side) 700 μm -500 μm -200 μm (18 degree blade angle ) than start collecting Hipocampus slices with 300 μm. according to these cutting parameters we can easily collect almost 7 to 9 slices with Hippocampus .
Sounds like you're cutting coronally... Not sure how helpful this is (I work with hamster), but you should be able to calculate approximate distance based on a published atlas. This is how I've determined slice distance in the past (to amygdala). Of course, you'd want to give yourself room for error and collect early - there are lots of variables which could impact that distance on an animal by animal basis.
Hope this is helpful!
Thank you both so much for your help! I found a published atlas and have been using that to help determine the depth. Thank you so much for taking time to respond to my question it really helped so much!
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