LLS Data Acquisition Guidelines

In order to improve reproducibility and repeatability of Lattice Light-Sheet (LLS) data across different experiments and instruments, a series of parameters and metadata need to be captured. A lot of the metadata requirements are similar to typical widefield and laser scanning microscopes, but some are specific to the LLS microscope. This documentation contains information for LLS operators/users to guide them in acquiring all the necessary pieces of information to aid in:

1. Configuring an LLS instrument to reproduce similar imaging conditions as those used for a given dataset
2. Configuring software to reproduce preprocessing procedures for a processed dataset.

The guidelines are split into two parts. The first part covers the general properties/metadata that should be captured for LLS experiments. These are not specific to a particular implementation of the LLS microscope.

The second part covers the specific elements that need to be captured using the Janelia implementation of the LLS microscope in order to cover the properties/metadata outlined in the first section.

Note: These guidelines are still evolving. If you have suggestions for other things that should be in the guidelines, we would encourage you to submit an issue on the llsm GitHub repository.