hybriss's Introduction

HybrISS

This repository includes the scripts and files assiciated with the HybrISS manuscript (https://www.biorxiv.org/content/10.1101/2020.12.02.408781v1)

Code found in this folder

Two main folders are present in this repository, incuding:

Preprocess: includes all the scripts used for (1) stiching the images, doing the maximum intensity projection and (2) detecting the spots and segmenting individual cells based on DAPI
Analysis: includes all the code used for, based on the segmented cells/spots, generate the figures presented in the manuscript. Each script has the name of the figure generated.

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hybriss's Issues

Pre-process pipeline and codebook generation

Hello,
first of all thanks for making this tool available. I have downloaded the ISS data and ran the example notebook. Everything went fine. I am wondering if you could possibly share the pre-processing tools and the codebook generation scripts. I am guessing you are using TissUUmaps for visualization?
thanks,
Alvaro

Cell Segmentaion

Hello @sergiomarco25 , thanks for your great work! I'd like to know how to do cell segmentation and to get the gene expression matrix using Python, CellProfiler, or R?

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