Vizgen Post-processing Tool for Cell segmentation

MERFISH technology identifies the location of transcripts across tissue sections with submicron precision. However, only localizing transcripts doesn’t provide a single-cell view of tissues. The Vizgen Post-processing Tool (VPT) uses cell segmentation methods to draw cell boundaries and generates single-cell output by combining the results with MERFISH data. With VPT, users can change methods of cell segmentation to better fit the data for improved single-cell analysis.

Download from GITHUB

Download a Sample Dataset

Dive into the intricate world of cell segmentation with our Vizgen Post-processing Tool (vpt). For users with knowledge of bioinformatics processes, this tool will assist in reanalyzing your  existing MERSCOPE® Platform  datasets, or conducting additional segmentation from your own custom plugin. To get started, utilize the sample data set below and follow along with a common use case.

Download Sample Dataset

Dataset Walk Through

Using the sample dataset, follow along to understand how to segment a dataset that is saved to the local harddrive. This will take you through the process of getting familiar with the tool and running a common segmentation use case.

Link to Vignette

Alternate Cell Segmentation

Experiment with alternative segmentation options (Methods, parameters, reprocess, or image channels)

Deep Learning Models

Use custom trained Deep-learning models on your dataset (Cellpose and Cellpose2)


Develop fully custom methods with the plugin architecture

Getting started with VPT

VPT runs on data generated by the MERSCOPE® Platform and conducts cell segmentation and other functions. Deployment is intended to be on a Linux server or a high-computing cluster.

Users trying to image smaller datasets and items can utilize a workstation.

System requirements

VPT can be run on a minimum system with the following criteria:

  • Processor: 11th Generation Intel® Core™ i7 Processor or equivalent
  • RAM: 16 GB or greater
  • SSD Capacity: Based on data size

For optimal performance, improvements to RAM size and additional CPU processing cores can reduce run time and system strain. VPT can be run on a system with the above capability, but may result in suboptimal and increased processing time, especially for large datasets.

Sign up to stay informed of updates to the VPT!

Interested in starting a MERFISH spatial profiling project at Vizgen? Fill out the form below and a member of the Lab Services team will get in touch within 2-3 business days to set up a project consultation call.

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Frequently Asked Questions