Speakers
Description
"Lightsheet microscopy is a rapidly developing and spreading technology that now enables imaging of very large, fixed samples such as adult mouse brains at single-cell. Previously, we developed the BigStitcher software that efficiently handles and interactively reconstructs large lightsheet acquisitions up to the terabyte range. However, new types of image acquisitions use modes such as stage-scanning lightsheet microscopy on expanded tissues of mice, monkey and eventually human samples, and pose new challenges in terms of dataset size and processing time. At the same time cloud-based processing is becoming standard.
Therefore, we developed BigStitcher-Spark (https://github.com/JaneliaSciComp/BigStitcher-Spark), which allows to run the entire BigStitcher pipeline distributed (local, cluster, cloud). It seamlessly switches between the BigStitcher GUI and distributed Spark execution, provides 10x faster fusion, and enables expert-user automation using the command line and easily accessible code.
In the workshop, we will teach how to use BigStitcher-Spark on smaller toy examples, which includes execution and viewing on the cloud for potentially massive parallel processing for very large datasets."
| Target audience | Advanced users, Intermediate developers, Advanced developers |
|---|---|
| Keywords | lightsheet microscopy, stitching, cloud processing |
