# A novel Slide-seq based image processing software to identify gene expression at the single cell level

## TL;DR

This paper introduces a new image processing software for Slide-seq that enables single-cell gene expression analysis using an affordable microscope.

## Contribution

The novel approach uses an inexpensive epifluorescence microscope for Slide-seq image analysis.

## Key findings

- The method uses DNA barcode beads to read RNA sequences from cells.
- Image processing includes stitching, registration, and base reading.
- The approach reduces the need for expensive confocal microscopes.

## Abstract

Analysis of gene expression at the single-cell level could help predict the effectiveness of therapies in the field of chronic inflammatory diseases such as arthritis. Here, we demonstrate an adopted approach for processing images from the Slide-seq method. Using a puck, which consists of about 50,000 DNA barcode beads, an RNA sequence of a cell is to be read. The pucks are repeatedly brought into contact with liquids and then recorded with a conventional epifluorescence microscope. The image analysis initially consists of stitching the partial images of a sequence recording, registering images from different sequences, and finally reading out the bases. The new method enables the use of an inexpensive epifluorescence microscope instead of a confocal microscope.