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DOI Python 3.7 License: GPL v3


Image acquisition software for mesoSPIM light-sheet microscopes. A mesoSPIM (mesoscale selective plane illumination microscope) is optimized for fast imaging of large (many cm³) cleared tissue samples at near-isotropic resolution. Currently, more than 20 mesoSPIM setups are operational around the world.

Parts lists, drawings, and instructions for building a mesoSPIM can be found in the mesoSPIM wiki.


The mesoSPIM is a versatile light-sheet microscope for imaging cleared tissue samples. It is compatible with all major clearing approaches and optimized for quickly creating large-field-of-view overview datasets.



  • Windows 7 or Windows 10, 64-bit
  • Python >=3.7, we recommend Anaconda

Device drivers



Installation steps

  1. Clone this repository either by via GitHub Desktop (recommended) or by downloading and unpacking the ZIP file into folder C:/Users/Public/mesoSPIM-control


  1. Open Anaconda prompt, create and activate a new environment mesoSPIM-py37:
conda create -p C:/Users/Public/conda/envs/mesoSPIM-py37 python=3.7
conda activate C:/Users/Public/conda/envs/mesoSPIM-py37
  1. Install mesoSPIM-specific libraries:
cd C:/Users/Public/mesoSPIM-control
pip install -r requirements-anaconda.txt


Anaconda prompt

  1. cd C:/Users/Public/mesoSPIM-control/mesoSPIM
  2. python (with argument -D for demo mode)

Desktop shortcut (fast launch)

From Anaconda prompt, type where conda, and enter the result (e.g. C:\Users\Nikita\anaconda3\Scripts\activate.bat) into line 10 of mesoSPIM.bat file:

"%windir%\System32\cmd.exe" /k ""C:\Users\Nikita\anaconda3\Scripts\activate.bat" "C:\Users\Public\conda\envs\mesoSPIM-py37" && python """

Save changes and double-click the mesoSPIM.bat file - this should launch the control software. If this does ot happen, check the Anaconda path. Once this works, create a shortcut and place it on your desktop for quick launching.

Prepare a configuration file and wire the hardware

The config files are stored in the mesoSPIM/config directory. The newly installed software will launch with the, which has all external hardware replaced with Demo simulated devices, to make sure installation is successful in "dry run".

If you have multiple config files you will be prompted to choose one that corresponds to your hardware.

Once your hardware is connected and turned on, change the Demo devices to hardware-specific names, set their parameters, and test each device. See Wiki for details.

Updating existing installation

To ensure safe transition to a new version, we recommend fresh installation of each new version into a separate folder (e.g. mesoSPIM-control-Nov2022) using the steps above. In order to unlock all new features, please review and add new sections from the demo config file to your old configuration file.

Documentation for users

For instructions on how to use mesoSPIM-control, please check out the documentation:

If you have questions, contact the current core developer Nikita Vladimirov.

How to cite this software

Fabian F. Voigt, Nikita Vladimirov, Christian Schulze, Rob Campbell, & Fritjof Helmchen. (2022). MesoSPIM control: An open-source acquisition software for light-sheet microscopy written in Python and Qt. Zenodo.