BakingTray
Search…
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.

Setting up multiple brains in BakingTray

    Set the cut size to a suitable value to accommodate the larger block.
    Set the image size to roughly what will be needed.
    After you have set the image size, find the ventral mid-line of the brain nearest the blade then press Set ventral midline.
    If you have four brains, use the front/right brain (or a space between the two right-hand brains) for setting the ventral midline. You will re-draw the box anyway, so it's not critical.
    Take a preview.
    All brains should be visible and reasonably framed. If not (as shown below) you will need to re-draw the box
    Re-draw and take the preview again
Drawing a box
    Once you are happy that the imaging area will capture all brains: hit Bake

Tips

    It is most efficient to image either two or four brains as these configurations leave the least empty space between the samples.
Last modified 1yr ago