Whole-cortex in situ sequencing reveals peripheral input-dependent cellular and area identity - perturbation

Published: 10 January 2024| Version 1 | DOI: 10.17632/5xfzcb4kn8.1
Xiaoyin Chen,


BARseq in situ sequencing data for 8 brains, with/without enucleation. Also provided scripts to reproduce figures in https://doi.org/10.1101/2022.11.06.515380. Accompanying manuscript: https://doi.org/10.1101/2022.11.06.515380


Steps to reproduce

Data: processed cell-based data and cubelet-based data. Needed to run all analysis. Image processing code: example code to process all data. The data from each brain was processed separately using the same set of code. Analysis code: Code to reproduce figures and analyses in the manuscript. MATLAB_functions: custom matlab functions used by the image processing and analysis code. README_github.md: README file for the associated software on github (see Related links) System requirements: The analysis code was run on a Windows 10 machine with MATLAB 2021b with image processing toolbox, parallel computing toolbox, statistics and machine learning toolbox, and bioinformatics toolbox. The image processing code was run on a Windows 10 machine with MATLAB 2021b with the same toolboxes as described above, Cellpose 2.2, bardensr 0.3.1, n2v 0.3.1, QuickNII 2.2 for Windows, Visualign 0.9 for Windows. Installation guide: Please follow installation instructions for MATLAB, Cellpose, bardensr, n2v, QuickNII, and Visualign. After installing, please unpack the matlab functions MATLAB_functions.zip and add the unpacked files to matlab path. Typical install time should not take more than 2 hours. Instructions: To reproduce analyses performed in the paper, unpack the data and analysis code files to the same folder and run. run time varies depending on the script, but should usually finish within minutes for each script.


Institut Pasteur, Allen Institute for Brain Science


High-Throughput Sequencing, New Sequencing Method, In Situ Methods