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VLab4Mic

A virtual lab to simulate fluorescence microscopy images, from molecular structures to acquisition, with no coding.

Simulationnapari plugin: experimentalFiji plugin: experimental

LabConstrictor-VLab4MicDocumentationWebsite

About

Build virtual samples from molecular structures, apply fluorescent labelling and simulate image acquisition across microscopy modalities, before stepping into the microscope room.

This is the desktop installer distribution of VLab4Mic. Two of its tools also run in napari and Fiji.

Works with

The authors say it works with:

  • Molecular structures: choose a PDB ID or provide a .cif/.pdb file; configure probe, labelling and acquisition
  • Image comparison: a reference and simulated 2D image with their pixel sizes (napari/Fiji tools)

Produces

The authors say it produces:

  • Simulated and noiseless fluorescence microscopy images, with their pixel size reported
  • Image comparison scores (SSIM and Pearson correlation) when using the comparison tool

Get it on your computer

Install the app on your own computer: download the installer for your system, and the steps for that system open below the buttons. You do this once; installing needs an internet connection, because the installer downloads the app's Python packages.

v0.1.7 · 15 October 2026 · files come from github.com/CellMigrationLab/LabConstrictor-VLab4Mic/releases

Windows

Windows installer307.0 MB · .exe

Installers built with LabConstrictor are not code-signed yet, so Windows may warn you. Run files only from this app's GitHub release. See the Windows steps.

macOS

Apple Silicon (M1 or later)181.1 MB · .pkgIntel189.2 MB · .pkg

Not sure which? Open the Apple menu, then About This Mac: Intel means Intel, M1 or later means Apple Silicon. If macOS refuses to open it, see the macOS steps.

Linux

Linux installer215.6 MB · .sh

Needs a terminal. Run it with: bash <file name>. See the Linux steps.

How to install on Windows
  1. Download the .exe file and double-click it.

  2. If Windows shows "Windows protected your PC", click "More info" and then "Run anyway". The installers are not code-signed yet.

    Windows protected your PC: click More info, then Run anyway

  3. Follow the on-screen prompts. Launch the app from the Start Menu or your desktop.

How to install on macOS
  1. Choose your file: open the Apple menu, then About This Mac. If the Chip or Processor says Intel, download the Intel installer; if it says M1, M2 or similar, download the Apple Silicon one.
  2. Double-click the .pkg file. If macOS refuses to open it, go to System Settings, Privacy & Security, scroll down to the message about the package and click "Open Anyway" (it appears only after you tried to open the file once). If you do not see it, try opening the file again, then check this page again.
  3. Follow the prompts (we recommend "Install only for me"). Launch the app from your Applications folder.
How to install on Linux
  1. Download the .sh file.
  2. Open a terminal in the download folder and run bash followed by the name of the file you downloaded, for example: bash MyApp-0.1.0-Linux-x86_64.sh
  3. Follow the prompts, then launch the app from your applications menu.

All systems, with pictures: Install an app.

Notebooks to open in your browser

These run on Google's servers in Google Colab: you need an internet connection and a Google account, and any data you load into the notebook is handled by Google. The desktop app runs on your computer.

Using it

  1. Install and launch VLab4Mic, then open the Welcome dashboard in JupyterLab
  2. Open VLab4Mic_main to select a molecular structure, fluorescent probe and imaging modality
  3. Run the acquisition and inspect the simulated and noiseless images
  4. Use VLab4Mic_parameter_sweeps when you need to compare multiple parameter combinations

For any LabConstrictor desktop app: after installing, open the app from the Start menu (Windows), the Applications folder (macOS) or your applications menu (Linux). A terminal window opens with it: keep it open while you work. Its Welcome notebook lists the app's notebooks; the notebook usage guide shows how to work with it.

Read more: Documentation.

Limitations

The authors say:

  • The napari and Fiji tools return one frame; multi-frame runs, parameter sweeps and advanced probe design require notebooks
  • In the default 1000 nm field a widefield image at 100 nm per pixel has only 10 x 10 pixels; raise Sample size XY

How to cite

The authors give this publication to cite: doi:10.64898/2026.06.02.729521

Read the paper

Name the version you used (latest release: v0.1.7 · 15 October 2026).

All downloads

Every installer of version 0.1.7 (7 files, with checksums)

Released 15 October 2026. Files come straight from the app's GitHub release.

Installers of the latest release
SystemFormatSizeFileSHA-256 (from GitHub)
Linux 64-bit (x86_64).sh215.6 MBVLab4Mic-0.1.7-Linux-x86_64.sh24400dd256c92d53c9450b637caa242d80accf0d418c5e59ce56155d58de4106
macOS (Apple Silicon).pkg181.1 MBVLab4Mic-0.1.7-MacOSX-arm64.pkg42300a6ca29685f3ac659a70921f7b64c50fbf1538b5ce2d7a68176ce57fe549
macOS (Apple Silicon).sh181.2 MBVLab4Mic-0.1.7-MacOSX-arm64.shd8e93e0cb47db0aed1bab06dd90235f550b8bb0513598acf4e031fc9b16090df
macOS (Intel).pkg189.2 MBVLab4Mic-0.1.7-MacOSX-x86_64.pkge6bf21f77ba1485858c09ce5e7a821fd197879793b9804eac797a60dd163a63e
macOS (Intel).sh189.2 MBVLab4Mic-0.1.7-MacOSX-x86_64.she7e2e8e6f85c36e6ee3b10787dd895ad8a837c43e0996413914a4611aa91618b
Windows 64-bit (Intel/AMD, x86_64).exe307.0 MBVLab4Mic-0.1.7-Windows-x86_64.exe18bc4143c5f3cccb752b8d51afd89d270d326e3138277acfbb7c2a1c277fa367
Windows 64-bit (Intel/AMD, x86_64).msi304.9 MBVLab4Mic-0.1.7-Windows-x86_64.msidf7aa0efd889aeeb865cac8714aa16de34d329eb363d7d4e040cd82629164ec7

Details

Kind
Simulation
Development status
Not stated by the authors
Latest release
v0.1.7 · 15 October 2026
License
MIT
Repository owner
CellMigrationLab
Also in (plugins)
napari plugin: experimental Fiji plugin: experimental
Topics
microscopy simulation, experiment design
Links
Homepage · Documentation · No issue tracker on GitHub

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