Serial Section Imaging at SWC
Using the equipment
We are currently only accepting internal users for BrainSaw, however we are actively working on solutions for external users also.
If you are generating no more than about a brain a month or rarely have brains then it's probably best to have brains run for you by another person in your lab or by the Facility. Users expecting to regularly generate at least about 3 to 4 brains a month can be trained to run them independently. Regardless of who runs your brains, you should have an intro session on the equipment and analysis approaches. There may be a long queue for training, so enquire well in advance. Feel free to shadow trained users from your lab, but you will still need to be formally trained before using the equipment.
Initial training on the serial section systems takes about 10 hours: typically there are 5 training sessions. Each session takes about 90 minutes. As part of this we will also discuss data handling and pre-processing (compressing data, transferring to server, registering, etc). You will need a minimum of 5 brains for initial training but we can get through up to about 10 or so if you have them. After these initial sessions you will book the equipment yourself and run samples under supervision until you feel confident to run independently.
How to sign up
- Fill in the training request form.
- If you've not done so already, start an account on the PPMS booking system.
Before your first training session
- Brains must be well perfused and undamaged, or they will not register well to the atlas. See our sample preparation notes and protocols
- Review the acquisition software user guide before your first training session.
- If you are unfamiliar with the Linux command line, please read this guide and try to get a little experience before training. You will need to use the command line to post-process your data.
- Once trained, book sessions via PPMS. Expect that you will need about 10 to 12 hours per brain for cell counting and about 6 to 8 hours for bulk projections or electrode tracks.
Citing
The BakingTray citation page describes how to cite BrainSaw and BakingTray, and also provides suggestions on how to structure the methods section.