Resources Hub

Histology User Guide for Preparing FFPE Samples for Experiments on the MERSCOPE and MERSCOPE Ultra Platforms. Rev B

This user guide provides a comprehensive, step-by-step protocol for preparing sectioned tissue samples using Vizgen’s MERFISH 2.0 chemistry for high-resolution spatial transcriptomics on the MERSCOPE platform. Rev A.

Histology User Guide for Preparing Fresh and Fixed Frozen Tissue Samples for Experiments on the MERSCOPE and MERSCOPE Ultra Platforms. Rev B

Rev A This guide outlines site requirements for installation of a MERSCOPE Ultra Instrument.

Rev B, April 2025

This guide outlines the instructions for use for the MERSCOPE Photobleacher. The MERSCOPE Photobleacher is used to remove autofluorescent background from tissue samples before performing MERFISH measurments on the MERSCOPE Platform.

User guide for the MERSCOPE Vizualizer.

Rev D, April 2024 This user guide is applicable to formalin-fixed paraffin-embedded (FFPE) tissue. It is not applicable to fresh frozen and paraformaldehyde (PFA)-fixed frozen tissue. It is also not applicable to fresh cultured cells….

This user guide is intended to guide users through a protocol to verify that their (user-provided) primary antibodies are compatible with MERSCOPE Protein Stain Kits, and that sample preparation will result in adequate protein imaging…

This notebook demonstrates how to use Scanpy to perform data pre-processing, dimensionality reduction, and single-cell Leiden clustering. This notebook is designed to take the Anndata output from the MERSCOPE Vizualizer and return a new Anndata…

Rev F, April 2024. This user guide explains how to properly prepare cultured cell samples to run on the MERSCOPE instrument and includes the protocol, materials, and technical tips.

This user guide explains how to verify that the RNA quality after sample preparation will result in adequate MERFISH imaging quality with the MERSCOPE Instrument. It includes the protocol, materials, and examples. 

Rev F, April 2024 This user guide explains how to properly prepare fresh and fixed frozen tissue sections to run on the MERSCOPE instrument and includes the protocol, materials, and technical tips.

Rev J, April 2025 This user guide contains the information needed for setting up, running, maintaining, and troubleshooting Vizgen’s MERSCOPE instrument.