Imaging multiple brains at once

You may image multiple brains at once. You will ask BakingTray to image a single large field of view that will incorporate all the brains. At the end of the acquisition you will use the sampleSplitter tool to break them up.

Setting up multiple brains in BakingTray

• We usually 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).
• Two brains we normally place in-line so the blade goes through the ventral surface of one, then through the ventral surface of the next.
• Ensure brains are at similar heights. Otherwise you will need to image a greater z extent than is necessary.
• If the agar blocks don't feel stable you can pour hot agar into the gaps to strengthen them into a single block.
• Set the image size to roughly what will be needed.
• Set the cut size to a suitable value to accommodate the larger block.
• Find the ventral mid-line of the brain nearest the blade then take a preview. You should see both brains in the preview.
• Ensure the imaging area will capture both brains then 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.
• If imaging four brains, you may want to cut laterally rather than ventral to dorsal.