Image acquisition software for mesoSPIM light-sheet microscopes. Compatible with all official versions of mesoSPIM hardware (Benchtop, v4, v5), and multple alternative configurations.
The mesoSPIM (mesoscale selective plane illumination microscope) is a family of versatile open-source microscopes optimized for fast imaging of large (many cm³) cleared tissue samples at near-isotropic resolution. Currently, more than 30 mesoSPIM setups are operational around the world. Parts lists, drawings, and instructions for building a mesoSPIM can be found in the wiki pages:
The mesoSPIM-control is python-based acquisition software with user-friendly GUI, based on PyQt5 framework.
- Windows >=7, 64-bit
- Python >=3.12, we recommend Miniforge and
mambapackage manager that comes with it. The Anaconda distribution is not recommended since the change of its terms of service in 2020. If you have existing Anaconda installation, you can still usecondainstead ofmambain the instructsions below.
Download and install the latest NI DAQmx drivers with default parameters.
- 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
PyVCAMPython 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:
pcopython 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
- Clone this repository either by via GitHub Desktop (recommended) or by downloading and unpacking the ZIP file into folder
C:/Users/Public/mesoSPIM-control
- Open Miniforge prompt, create and activate a new environment
mesoSPIM-py312:
mamba create -p C:/Users/Public/mamba/envs/mesoSPIM-py312 python=3.12
mamba activate C:/Users/Public/mamba/envs/mesoSPIM-py312
- Install mesoSPIM-specific libraries:
cd C:/Users/Public/mesoSPIM-control
pip install -r requirements-conda-mamba.txt
cd C:/Users/Public/mesoSPIM-control/mesoSPIMpython mesoSPIM_Control.py(with argument-Dfor demo mode)
From Miniforge prompt, type where mamba, and enter the result (e.g. C:\Users\Nikita\miniforge3\Scripts\activate.bat) into line 10 of mesoSPIM.bat file:
"%windir%\System32\cmd.exe" /k ""C:\Users\Nikita\miniforge3\Scripts\activate.bat" "C:\Users\Public\conda\envs\mesoSPIM-py312" && 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-Jan2025) 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.
Some errors during software startup and acquisition can be displayed in the mamba/conda terminal, while a highly detailed log will be recorded in the time-stamped file in mesoSPIM/log folder. This log file is individual for each session, named by date and time of software start-up, eg mesoSPIM/log/20241210-154845.log.
For instructions on how to use mesoSPIM-control, please check out the documentation:
- ZMB (Univerity of Zurich) guides on mesoSPIM start-up, setting up, and acquisition
- PPT (outdated version),
- 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