Mar 27, 2026
Histology - Microtome
- Maria Dima1,2,
- Talia Lerner3
- 1Northwestern University;
- 2Lerner Lab;
- 3Northwestern
Protocol Citation: Maria Dima, Talia Lerner 2026. Histology - Microtome. protocols.io https://dx.doi.org/10.17504/protocols.io.n92ld41ynl5b/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 26, 2026
Last Modified: March 27, 2026
Protocol Integer ID: 313983
Keywords: #histology, #slicing, #cryotome, #frozen_microtome, #dryice, frozen microtome, tissue for histology purpose, microtome, histology purpose, histology, tissue
Abstract
How to use the frozen microtome to slice your tissue for histology purposes.
Troubleshooting
Materials
10m
All things can be found in histology room except for dry ice:
- slicer
- slicing platform
- tools
- razors one for slicer (in blue box) and one for cutting tissue (from drawer)
- 100mm plate
- 12 well plate with PBS
- 24 well plate with cryoprotectant
- cryoprotectant (from 4 degree fridge)
- paper towel
- paint bruhes
- OCT
- tin foil cover
- tin foil (from drawer)
- ethanol
For dry-ice:
By the slicer you will find the folder "Lerner Lab- Microtome Log"
When you open it up you will find this paper titled "Microtome sectioning protocol" that has intructions on how to get dry ice
- Grab the red bucket from the histology room
- Go to the first floor in Ward, walk towards Superior Street and on the right of the hall you'll see a door saying "loading dock" you should go through
- There are big blue coolers that you can open and grab as much dry ice as you need from
- Bring the bucket with the ice to room 1-714
- Turn on the scale, weigh the bucket with the ice and subtract 0.5 for the bucket
- On the computer next to the scale, complete a dry ice order:
> Lab phone extension: 35658
> Startup chartstring: 172
5108000
10043326
01
- You can complete the order and take the ice back to lab
10m
Setup
18m 13s
Mount slicing platform on slicer and tighten it up with the tool
1m
Move the orange protector to the right to mount the blade with the other tool by screwing in the screws
5s
Pour enough ethanol into the tray of the slicing platform to cover the bottom and add lots of dry ice
5s
Grab your tissue and place it on the petri dish. With a blade cut the cerebellum as even and level as possible.
5m
Add a dime-sized blob of OCT onto the clicing platform. Wait for the OCT platform to freeze and before the very top of it is fully frozen place the tissue with the cerebellum-cut side on the OCT and the olfactory bulb facing up.
5m
Cover the brain and OCT with the tin foil cover until the brain looks frozen
7m
While you are waiting for the brain to freeze, fill the 12 well plate with PBS and the 24 well plate with cryoprotectant (1-2ml/well) and label
Once the brain is frozen, bring down the latch on the side of the slicer to be able to move the blade back and forth
and adjust the thickness to what you want the slices to be.
Make sure to turn the slice knob enough so that when you start cutting, the blade is at the top of the olfactory bulb and not the middle of the brain.
Keep adding dry ice so that the OCT does not melt or the brain does not become too soft, but find a balance because if you add too much and it gets too cold, the OCT might detach from the platform, or the brain slices might come out broken
3s
Slicing
5m 10s
With every slice, stop at the front and use the brush to pick it up and transfer it to the well plates (cryoprotectant if for longer storage, PBS if short-term storage). If you do not need the slice, pick it up with the brush and place it on the paper towel.
Make sure that if your virus has a fluorescent tag, you cover the well plates with the slices
10s
If the OCT comes off the platform you have to wait until the temperature comes down to remove the brain and start over.
If you use the platform and need more space for the next brain you also wait until the OCT and the cut brains get to room temperature to remove them. Then, bring the platform back down with dry ice and repeat with OCT and the new brain.
Once you are done place the plate with the cryoprotectant in the -20 degrees fridge and the one with the PBS in the 4 degrees fridge in the histology room.
5m
Clean-up
12m 5s
Remove the platform and clean it in the sink. Make sure all of OCT is removed. Let it dry
5m
Clean any tools you used, along with the brushes, and let them dry
5m
Throw away the blades in the red sharps bin
5s
Wipe down the slicer with ethanol
2m