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 15 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

• Hamamatsu Orca Flash 4.0 V2/V3 camera: Hamamatsu DCAM API. To test camera functionality, HCImage can be used.
• Photometrics camera: PVCAM and PVCAM-SDK. In addition, the PyVCAM Python package is required (github), which depends on ¨MS Visual C++ 14.0 or higher. When installing the MS Visual C++ tools, make sure to check C++ build tools
• PCO camera: pco python library (python -m pip install pco). A Version ≥0.1.3 is recommended.

• PI stages: Software for Physik Instrumente stages. To test the stages, PI MicroMove can be used.
• Steinmeyer Mechatronics / Feinmess stages: Software for using Galil drivers if such a stage is used. To test the stages, GalilTools can be used.
• ASI stages: ASI Tiger drivers. If using USB connection, check ASI instructions on USB support

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

2. 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

3. Install mesoSPIM-specific libraries:

cd C:/Users/Public/mesoSPIM-control
pip install -r requirements-anaconda.txt

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

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 "mesoSPIM_Control.py""

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.

The config files are stored in the mesoSPIM/config directory. The newly installed software will launch with the demo_config.py, 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.

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.

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

• PPT,
• youtube channel,
• subscribe to our mailing list.

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

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. https://doi.org/10.5281/zenodo.6109315