README.md

Install notes for Needles

Designed for Matlab R2016b+. Earliers versions need to install the Json lab toolbox https://github.com/fangq/jsonlab.

Download the atlas files into a directory of your choice:

For Allen CCF Atlas at 50 µm resolution (IBL's default)

You will need the average_template and the annotation volume. For IBL, files are in google drive / WG-Physiology/Resources/Brain Atlases/Allen50:

• https://drive.google.com/drive/u/0/folders/1x9zVNWtUofVA0FTmCKPwQcj2PbH_wBoD

Files are also publicly available from the Allen Brain Institute servers:

• http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/

For the "DSURQE" MRI atlas (used previously, and used for calibration)

• http://repo.mouseimaging.ca/repo/DSURQE_40micron_nifti/DSURQE_40micron_average.nii
• http://repo.mouseimaging.ca/repo/DSURQE_40micron_nifti/DSURQE_40micron_labels.nii
• http://repo.mouseimaging.ca/repo/DSURQE_40micron/DSURQE_40micron_R_mapping.csv

For more information, http://www.mouseimaging.ca/technologies/mouse_atlas/C57Bl6j_mouse_atlas.html

Clone or download the WGs repository

• Clone or download the WGs repository (https://github.com/int-brain-lab/ibllib-matlab)
• Within the WGs/Physiology repository, edit the ./ibllib-matlab-master/needles/needles_param.json file.
• Set the path_atlas to the folder in which you did download the 3 files mentionned above.
  For example: "path_atlas": "/datadisk/BrainAtlas/ATLASES/",
  Windows users need to "escape" backslashes this way:
  "path_atlas": "C:\\path\\to\\my\\folder",

Setup the Matlab Path and run

For general use without worrying about the path, run Run_Needles.m file in Matlab

For advanced use with a non-frozen ibllib library, set your paths to:

• ./ibllib-matlab-master/needles/
• the ibllib Matlab library

Usage

A blank window should have appeared by now.

• click on File > Load. This will fetch and display the Atlas you did download. The "IBL50" atlas is the main one to use.
• click and remain clicked on the AP line on the axial window and move to find a coronal plane
• click on one of the white dots to jump to the corresponding coronal plane.