Package: mesospim-control
mesoSPIM-controlImage acquisition software formesoSPIMlight-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 operationalaround the world.Parts lists, drawings, and instructions for building a mesoSPIM can be found in themesoSPIM wiki.OverviewThe 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.InstallationPrerequisitesWindows 7 or Windows 10, 64-bitPython >=3.7Device driversCamerasHamamatsu Orca Flash 4.0 V2/V3 camera:Hamamatsu DCAM API. To test camera functionality,HCImagecan be used.Photometrics camera:PVCAM and PVCAM-SDK.
In addition, thePyVCAMPython package is required (github),
which depends on ¨MS Visual C++ 14.0 or higher.
When installing the MS Visual C++ tools, make sure to checkC++ build toolsPCO camera:pcopython library (python -m pip install pco). A Version ≥0.1.3 is recommended.StagesPI stages:Software for Physik Instrumente stages. To test the stages, PI MicroMove can be used.Steinmeyer Mechatronics / Feinmess stages:Software for using Galil driversif 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 onUSB supportAnacondamesoSPIM-control is usually installed fromAnaconda.Create and activate a new environmentmesoSPIM-py37from Anaconda prompt:conda create -p C:/Users/Public/conda/envs/mesoSPIM-py37 python=3.7
conda activate C:/Users/Public/conda/envs/mesoSPIM-py37InstallmesoSPIM-controlfrom PyPi:pip install mesospim-controlThe code will be installed inC:\Users\Public\conda\envs\mesoSPIM-py37\Lib\site-packages\mesoSPIMdirectory.LaunchingDesktop shortcutFor the end users we recommend this method.
Find filesmesoSPIM.batandmesoSPIM-shortcut.lnkin the..\mesoSPIM\directory defined above.
Copy themesoSPIM-shortcut(one with blue-orange icon) to your desktop.
Double-clicking the shortcut will launch themesoSPIM-control.Anaconda prompt (alternative)Activate the environmentconda activate C:\Users\Public\conda\envs\mesoSPIM-py37Launch themesospim-controlfrom any directory:mesospim-controlOr, navigate to folderC:\Users\Public\conda\envs\mesoSPIM-py37\Lib\site-packages\mesoSPIMand runpython mesoSPIM_Control.pyThese methods are recommended for developers - they require more steps but allow more control,
since you can move themesoSPIMfolder to where you like in your file system.Prepare a configuration file and wire the hardwareThe config files are stored in themesoSPIM/configdirectory.
The newly installed software will launch with thedemo_config.py,
which has all external hardware replaced withDemosimulated devices, to make sure installation is successful in "dry run".Tip: another quick way to start in demo mode from command line (for developers):python mesoSPIM_Control.py -DIf 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 theDemodevices to hardware-specific names, set their parameters, and test each device.
SeeWikifor details.TroubleshootingIf there are problems with PyQt5 such asModuleNotFoundError: No module named 'PyQt5.QtWinExtrasafter startingmesoSPIM-control, try reinstalling PyQt5 by:python -m pip install --user -I PyQt5andpython -m pip install --user -I PyQt5-sip)Updatingconda activate C:\Users\Public\conda\envs\mesoSPIM-py37
pip install --upgrade mesospim-control:warning: If you are updatingmesoSPIM-controlfrom a previous version, please add new sections from thedemo config fileto your old configuration file in order to unlock all new features.Documentation for usersFor instructions on how to use mesoSPIM-control, please check out the documentation:PPT,youtubechannel,subscribe to ourmailing list.If you have questions, contact the current core developerNikita Vladimirov.How to cite this softwareFabian 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