Post Mortem Imaging

Imaging and Associated Data Analaysis and Techniques

After NISSL staining and mounting our sections (which is currently the terminal step for pretty much all of our lab's experiments) we must visualize the brain to either verify our coordinates or verify our lesions or whatever. Thus the pipeline is 1) do experiment (ephys, Ca2+ imaging, lesion) 2) Euthenize and perfuse animal 3) Process tissue / do histology 4) Scan slides and Analyze Histology (post-mortem imaging).

See the Wet Lab pages for information about doing histology.

Scanning

We use the Baymax slide scanner at the MIC. Access to the MIC is arranged by following these steps:

1. Attend a Microscopy Training Lecture (1.5 hours), offered once a month. See the schedule HERE.
2. Fill out the MIC User Registration Form HERE.
3. Sign-up for an iLabs account HERE.
4. Once you have your sample(s) ready, email Holly ([email protected]) or Feather ([email protected]) to set up a date for hands-on training (usually 2 hours - some instruments take more, a very few take less).
5. Read the MIC_Rules & Regulations, to which all users must adhere.
6. The door code is 349198

Saving the Data and Storage

• After scanning on Baymax, take the data back to the lab on an external hard drive.
• Long term storage should be on the lab's google drive, but the most useful place for the data to be is the TDrive (/auto/tdrive/Histology Images). Hopefully we have enough storage on it still.
• The google drive location is "TLab Notebooks > Histology" -- There is also a spreadsheet in that same location where things should get written down.

Analysis

• Analysis can be done with FIJI or with Zen, the Zeiss software that is also used for image capture on the BayMax. The lab does not have its own copy of Zen software, which runs on Windows machines. However, there is a computer with Zen Blue in Room 230 in LKS. If you have been trained to use Morpheus through the MIC, you can use this computer and get access to Room 230. The password for the Morpheus Processing Only computer is Morpheus2016. Reserve through iLabs.

Links to the MIC

https://my.ilabsolutions.com/

Links to other places

We also can use the biological imaging facility (BIF- microscopy.berkeley.edu), which has less microscopes and they are significantly older, than the MIC. They are in Kincaid and well maintained. web login: BIF : BIF2021, computer login: theunissenlan / f1nch

Instructions here

Whole brain clearing techniques (CLARITY, CUBIC, etc)