# Vizgen

> Vizgen is a spatial biology company building integrated spatial multiomics platforms for
> single-cell research. Its MERSCOPE and MERSCOPE Ultra instruments use MERFISH imaging-based
> spatial transcriptomics to map up to 1,000 RNA targets in intact tissue at subcellular
> resolution, complemented by InSituPlex multiplex protein immunofluorescence assays (OmniVUE
> and custom U-VUE panels) and the STARVUE analysis software.

Important: Vizgen publishes **no public REST, GraphQL, gRPC, MCP, or webhook API**. As of
2026-08-05 there is no api.vizgen.com, no docs.vizgen.com, no developer portal, and no
`/.well-known/*` discovery document on vizgen.com. Its public developer surface is
open-source data tooling on GitHub and PyPI. Do not attempt to call a Vizgen web API — there
is none to call.

This file was generated by API Evangelist from the Vizgen public surface; Vizgen does not
publish an llms.txt of its own (https://vizgen.com/llms.txt returned 404 on 2026-08-05).

## Developer surface

- [Vizgen Post-processing Tool (VPT) documentation](https://vizgen.github.io/vizgen-postprocessing/): Sphinx documentation for the Apache-2.0 command-line toolkit that reprocesses MERSCOPE single-cell outputs.
- [VPT installation](https://vizgen.github.io/vizgen-postprocessing/installation.html): pip, Docker (`vzgdocker/vpt`), and Poetry install paths; Python >=3.9,<3.11.
- [VPT command line interface](https://vizgen.github.io/vizgen-postprocessing/command_line_interface/index.html): the 13 `vpt` sub-commands and their arguments.
- [Segmentation options](https://vizgen.github.io/vizgen-postprocessing/segmentation_options/index.html): Watershed, Cellpose, Cellpose2, CellposeSAM, and InstanSeg families, plus benchmarks.
- [Segmentation algorithm JSON file format](https://vizgen.github.io/vizgen-postprocessing/segmentation_options/json_file_format.html): the machine-readable specification document `vpt run-segmentation` consumes.
- [Output data formats](https://vizgen.github.io/vizgen-postprocessing/output_data_formats/index.html): detected transcripts, entity-by-gene matrix, entity metadata, geometry file, and VZG file formats.
- [Plugin architecture](https://vizgen.github.io/vizgen-postprocessing/experimental_features/plugin_architecture.html): how third-party segmentation algorithms register with VPT.
- [Analysis vignettes](https://vizgen.github.io/vizgen-postprocessing/analysis_vignettes/index.html): worked end-to-end examples.

## Code and packages

- [Vizgen on GitHub](https://github.com/Vizgen): the Vizgen organization — VPT, its plugins, and tutorial notebooks.
- [vizgen-postprocessing](https://github.com/Vizgen/vizgen-postprocessing): the VPT source, Apache-2.0.
- [vpt on PyPI](https://pypi.org/project/vpt/): `pip install vpt` — v1.3.3.
- [vpt-core on PyPI](https://pypi.org/project/vpt-core/): importable core library shared by VPT and its plugins.
- [vzgdocker/vpt on Docker Hub](https://hub.docker.com/r/vzgdocker/vpt): reproducible VPT environment with Nextflow and AWS CLI v2.
- [Segmentation plugins](https://vizgen.github.io/vizgen-postprocessing/segmentation_options/index.html): `vpt-plugin-watershed`, `vpt-plugin-cellpose`, `vpt-plugin-cellpose2`, `vpt-plugin-cellposesam`, `vpt-plugin-instanseg`.
- [Releases](https://github.com/Vizgen/vizgen-postprocessing/releases): semver releases cut by python-semantic-release.

## Products and science

- [Products](https://vizgen.com/products/): MERSCOPE Ultra, spatial transcriptomics assays, InSituPlex protein panels, STARVUE software.
- [Technology](https://vizgen.com/technology/): MERFISH 2.0 imaging-based spatial transcriptomics.
- [Applications](https://vizgen.com/applications/): neuroscience, oncology, immunology, cell atlasing.
- [Services](https://vizgen.com/services/): Vizgen-run spatial profiling services.
- [Publications](https://vizgen.com/resources/publications/): peer-reviewed work using the platform.
- [Data Release Program](https://vizgen.com/data-release-program/): publicly released MERSCOPE datasets.
- [Resources](https://vizgen.com/resources/): user guides, protocols, and application notes.

## Company

- [News](https://vizgen.com/news/)
- [Events](https://vizgen.com/events/)
- [About Us](https://vizgen.com/about-us/)
- [Careers](https://vizgen.com/careers/)
- [Support](https://vizgen.com/vizgen-support-vizgen/)
- [Contact](https://vizgen.com/contact/)

## Optional

- [Terms of Use](https://vizgen.com/terms-of-use/)
- [Privacy Policy](https://vizgen.com/privacy-policy/)
- [API Evangelist profile](https://apis.io/provider/vizgen/): independent third-party profile of this company's public developer surface.