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Nick Steinmetz edited this page Aug 25, 2019 · 3 revisions

Tracks are not necessarily easy to observe in simple nissl- or DAPI-stained slices. Therefore, labeling with DiI, a fluorescent dye, is recommended. Dip the probe in DiI, let it dry, and repeat. If it is inconvenient to dip the whole probe, the dye can also be applied by using a micropipette, holding a drop on the end of it and running the drop over the stationary probe several times. Usually you will be able to see the probe take a pink color when the light catches it at the right angle, after the DiI has been successfully applied.

Normal DiI or other colors (e.g. DiO, DiD) can be used for normal histology. If tissue clearing will be used, a modified version of DiI can be used instead.

To align histological slices to a reference atlas, one open source and publicly available software designed for this purpose is SHARP-Track. See the bioRxiv paper for more details.

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