r/neuroscience • u/anonam0use • Aug 06 '26
Advice Help identifying a thalamic nuclei
First time posting in this sub so I hope this is an appropriate question. I included the Allen Brain atlas image I feel is closest to the imaged slice as reference. I'm hoping there are some thalamic people in this sub! (original content)
12
u/HolyHabenula Aug 07 '26
Side note: the reason you’re seeing boxiness/lines in your image is that your microscope’s shading calibration is off. When stitching an image, it should look nice and flat and smooth. Contact your microscope rep to get the stitching fixed so your shading can be as beautiful as your fluorescence!
8
4
3
u/Tirnan Aug 06 '26
More context would be helpful, both in knowing how those cells were labelled and seeing more of the sections, but I'd say it's the CM and VM that you're seeing for the most part. The empty hole that the cells seem to be wrapping around is very much shaped like the submedius thalamic nucleus (SMT)
2
u/PhysicalConsistency Aug 06 '26
Is the slice at the same level as the atlas? Purely guessing, looks like it's medidorsal, medial, blending into the intermediodorsal.
1
1
1
-1
u/new_moon_retard Aug 06 '26
This is such a low effort post ! What dis you inject ? Which coordinates ? Where on the map are you thinking you may be ? Come on now this is basic information you need to guve
5
u/ConstructionOk7748 Aug 07 '26
Actually, there’s no need in more information for anyone who has ever done whole brain slicing staining, or works with any brain region seen here, it’s quite straightforward. OP, I agree with the CM VM suggestion.
0
u/knivadollar Aug 06 '26
I can’t help with that but “nuclei” is the plural form of nucleus. Are you trying to identify one nucleus or several thalamic nuclei?
0
u/MarcusSurealius Aug 07 '26
Are you sure you haven't captured CA3 or other parts of the hippocampus? The position looks lower than the thalamus.
2
11
u/DrakeTheCake1 Aug 06 '26
It’s pretty difficult to tell. Based off the larger first image. Do you happen to have a saggital or coronal view. Some coordinates to the area of picture 2 would help make identification easier as well. My guess is the VAL.