Imaging multiple brains at once

You may image multiple brains (or other samples) at the same time. The basic way of doing this is to select one large field of view that will incorporate all the samples. At the end of the acquisition you will use the sampleSplitter tool to break them up into separate sample directories.
Before reading this page you should already be familiar with the instructions in the main user guide and know how to set up a single sample.

Mounting multiple samples

  • You can mount brains separately in agar then trim the agar blocks so that they are as close together as possible. (e.g. within a couple of mm).
  • If the agar blocks don't feel stable you can pour hot agar into the gaps to strengthen them into a single block.
  • As an alternative to the separate blocks, you can stack brains on top of each other in the same agar mold by supporting them with thin metal wire (such as guitar string) inserted via holes drilled in the sides.
  • Four brains are placed in a 2 x 2 arrangement.
  • Two brains are perhaps best placed in-line so the blade goes through the ventral surface of one, then through the ventral surface of the next. This means more cutting time but you worry less about blade tilt. Side by side also works.
  • Ensure brains are at similar heights. Otherwise you will need to image a greater z extent than is necessary.
Ensure you make a record of which brain is which for when you split them up later on. It's easy to get confused, so take your time and make notes or take photos as you go.


  • It is most efficient to image either two or four brains as these configurations leave the least empty space between the samples.