Emmett James Thompson

(Adapted from code by Hernando Martinez: https://github.com/HernandoMV)

sequences histology

script for producing projections of probe placements on the allen standard space atlas

See our publication for more details: Replay of Procedural Experience is Independent of the Hippocampus.

Overview

This repository includes:

• example data file for labelled probe start and end points
• sagital and coronal allen standard space atlas images
• an example analysis script that projections of probe placements on the allen standard space atlas

Prior steps...

To produce data for this analysis follow these steps:

1. implant a probe coated in dye
2. Prepare histology (perfusion)
3. Image the enitre brain with serial section microscopy (eg. SWC brainsaw)
4. Register the aquired images to the allen standard space with brainreg: https://brainglobe.info/documentation/brainreg/index.html
5. Use fiji or napari to manually find the xyz coordinates of the start and end of each probe track (coordinates in the allen standardised space)
6. add these coordinates to a txt file like the one provided in example data

Requirements

Ensure you have the following software installed:

• Git
• Python (Version used: 3.12.3)
• Jupyter notebook
• this analysis requires some standard (very easy to install) python packages