mesospim-control 1.8.0

mesoSPIM microscope control

mesoSPIM-control

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.

Overview

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.

Installation

Prerequisites

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

Device drivers

Cameras

• 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.

Stages

• 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

Anaconda

mesoSPIM-control is usually installed from Anaconda.

1. Create and activate a new environment mesoSPIM-py37 from Anaconda prompt:

conda create -p C:/Users/Public/conda/envs/mesoSPIM-py37 python=3.7
conda activate C:/Users/Public/conda/envs/mesoSPIM-py37

2. Install mesoSPIM-control from PyPi:

pip install mesospim-control 

The code will be installed in C:\Users\Public\conda\envs\mesoSPIM-py37\Lib\site-packages\mesoSPIM directory.

Launching

Desktop shortcut

For the end users we recommend this method. Find files mesoSPIM.bat and mesoSPIM-shortcut.lnk in the ..\mesoSPIM\ directory defined above. Copy the mesoSPIM-shortcut (one with blue-orange icon) to your desktop. Double-clicking the shortcut will launch the mesoSPIM-control.

Anaconda prompt (alternative)

Activate the environment

conda activate C:\Users\Public\conda\envs\mesoSPIM-py37

Launch the mesospim-control from any directory:

mesospim-control

Or, navigate to folder C:\Users\Public\conda\envs\mesoSPIM-py37\Lib\site-packages\mesoSPIM and run

python mesoSPIM_Control.py

These methods are recommended for developers - they require more steps but allow more control, since you can move the mesoSPIM folder to where you like in your file system.

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 demo_config.py, which has all external hardware replaced with Demo simulated 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 -D

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.

Troubleshooting

If there are problems with PyQt5 such as ModuleNotFoundError: No module named 'PyQt5.QtWinExtras after starting mesoSPIM-control, try reinstalling PyQt5 by: python -m pip install --user -I PyQt5 and python -m pip install --user -I PyQt5-sip)

Updating

conda activate C:\Users\Public\conda\envs\mesoSPIM-py37
pip install --upgrade mesospim-control 

:warning: If you are updating mesoSPIM-control from a previous version, please add new sections from the demo config file to your old configuration file in order to unlock all new features.

Documentation for users

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.

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