Sashimi

Sashimi is a user-friendly software for efficient control of digital scanned light sheet microscopes (DSLMs). It is developed by members of the PortuguesLab at the Technical University of Munich and Max Planck Institute of Neurobiology. Sashimi relies on the fast, multidimensional Napari viewer.

While built for a particular microscope configuration, the modular architecture allows for easy replacement of hardware by other vendors (we will help with and welcome contributions for supporting other cameras, boards and light sources).

Installation

Install the latest Anaconda distribution of Python 3.

Clone this repository and navigate to the main folder ../sashimi

Recommended: Create a new environment

It is a good practice to create an environment for every project. The provided environment.yml sets up almost all required dependencies (see below).

conda env create -f {path to environment.yml}

You can activate the environment by running:

conda activate sashimi

After this you moght have to install two extra dependencies for controlling a Cobolt laser:

pip install pyvisa
pip install pyvisa-py

Install with pip

For a non-editable installation run:

pip install .

Otherwise, if you want to contribute to the project as a developer, for editable installation run:

pip install -e .

Now you are ready to go!

Configuring sashimi

Sashimi includes the sashimi-config module that lets you interact with the hardware and software settings from command line. You can display the current configuration of the system.:

sashimi-config show

You can ask sashimi for help:

sashimi --help

More information on its usage can be found by asking sashimi-config for help:

sashimi-config --help

You can add and modify parameters just from the command line. For example, to set the piezo waveform readout channel to Dev1/ao0:0 just run:

sashimi-config edit -n z_board.write.channel -v Dev1/ao0:0

Or to modify the minimum and maximum voltage (in Volts) of the channel:

sashimi-config edit -n piezo.position_write.min_val -v 0
sashimi-config edit -n piezo.position_write.max_val -v 10

Starting the software from command line

Open a new anaconda prompt and activate your environment like above. Then run:

sashimi

Add the option --scopeless:

sashimi --scopeless

If you want to run the software with mock hardware, such as for debugging or developing.