AllenNeuralDynamics / exa-spim-control

Acquisition control for the exaSPIM microscope system

exa-spim-control

Acquisition control for the exaSPIM microscope system

Prerequisites

This program has substantial platform memory requirements (~103 GB for 4 channel imaging). These ram requirements are largely due to the chunk size of the online compressor (ImarisWriter) which performs best with larger chunks. Recommended requirements are:

• CPU with 8 cores
• 128 GB of ram, ideally on a single memory card

Installation

From this folder install this python package with:

pip install -e .

There are a few additional software components to install. Read on for installation instructions.

Manual Components

eGrabber

You will need egrabber for coaxlink and gigelink installed for your particular system. Note that, to download the egrabber sdk, you will first need to make an account with them. After downloading and installing eGrabber, you will need to install the eGrabber python package (stored as a wheel file). For more info installing the python whl file, see the notes from Euresys.

Generally, the process should be as simple as finding the whl package in the eGrabber subfolder and invoking:

pip install egrabber-22.05.3.77-py2.py3-none-any.whl

Note that the above version above be slightly different.

eGrabber

On Linux you will also need to compile and install ImarisWriter. Note that, additionally, the PyImarisWriter.py file installed with pip may be out of date and need to be replaced with the latest version on Github. Otherwise, you may get a segfault.

TODO: is this the right way to do this?

After compiling ImarisWriter on Linux, it needs to be recognized system-wide with:

sudo make install
ldconfig -n /abs/path/to/ImarisWriter/release/lib

Run

as an executable

This method is convenient for launching the code on a PC plumbed with all the necessary hardware (Camera, galvos, etc.). A thin prompt-based UI is exposed for interacting with the machine.

With the package installed, you can launch the code from a command prompt by invoking exaspim. This will run the exaspim with a config.toml file in the current directory. To specify a config.toml file located elsewhere, use:

exaspim --config /path/to/config.toml

It may be useful to run the package in "simulated" mode, which will dry-run the data acquisition loop on fake images with parameters from a config file. All hardware connections are spoofed. This mode is useful for tweaking config values like the ImarisWriter "chunk size" and ensuring that your pc has enough ram and disk space to run an acquisition.

exaspim --simulated

It is also possible to change the output log level:

exaspim --log_level DEBUG

As a Package

This method is convenient for developing GUIs on top of the Exaspim class for interacting with the machine as a production instrument.

from exaspim.exaspim import Exaspim
from exaspim.exaspim_config import ExaspimConfig

cfg = ExaspimConfig("config.toml")
instrument = Exaspim(cfg)
instrument.run()