Skip to content


Switch branches/tags

Latest commit


Git stats


Failed to load latest commit information.
Latest commit message
Commit time

Automated Library prep for Spatial Transcriptomics

This repository contains the scripts necessary to run the Spatial Transcriptomics library preparation on a Magnatrix 8000+. The technology has been described by Ståhl and a description of the automation is available here:

Programs included

Spatial Transcriptomics

Two programs are included. The first allows for parallel preparation of 1 to 8 samples and a second higher throughput program capable of preparing up to 16 samples. Each program consists of two parts. The first part takes the cDNA from the Spatial Transcriptomics array and outputs the amplified RNA that is used as input in the second part. The second part of the programs outputs a sequencing library that is ready for multiplex library indexing.

Spatial Genomics

Beta version of the Spatial Genomics protocol. Not tested.

Installation using the import function in Magnatrix OS

Download the ST_AMF.HXP file and log in to Magnatrix OS as a power user or administrator.

  • To install all protocols right click on the Applications bar on the top left part and choose Automatic import. Select ST_AMF.HXP and press Open.
  • To install selectively use the Import Guide, found in the Tools menu. Select ST_AMF.HXP as the import file and then select the AMF file you want to import the protocols to. Follow the on screen instructions.

Manual installation

  1. Open the AMF/PGF editor in Magnatrix OS.
  2. Choose whether to create a new PFG file or modify an existing.
  3. Create a new Holder file for each part of the two programs.
  4. Open the Holder editor and set the path for each downloaded file.

Points on transferring the programs to other liquid handling robots

Currently the automated protocol is only available on the Magnatrix platform. Other programs originally written for the Magnatrix system has been successfully transferred to the Agilent NGS workstation (


The automated protocols for Spatial transcriptomics






No releases published


No packages published