Open-source image analysis pipeline with 100+ fold speed-up and real-time compression (Conference Presentation)

Jules Scholler; Joel Jonsson; Tomas Jorda-Siquier; Ivana Gantar; Laura Batti; Stephane Pages; Christophe M. Lamy; Ivo F. Sbalzarini

doi:10.1117/12.2647105

15 March 2023 Open-source image analysis pipeline with 100+ fold speed-up and real-time compression (Conference Presentation)

Jules Scholler, Joel Jonsson, Tomas Jorda-Siquier, Ivana Gantar, Laura Batti, Stephane Pages, Christophe M. Lamy, Ivo F. Sbalzarini

Author Affiliations +

Proceedings Volume PC12385, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXX; PC1238509 (2023) https://doi.org/10.1117/12.2647105
Event: SPIE BiOS, 2023, San Francisco, California, United States

Abstract

We propose an end-to-end image analysis pipeline based on the Adaptive Particle Representation (APR) for analyzing large 3D cleared tissue samples such as whole mouse brains or large human brain sections, achieving 100+ times faster computation. Our pipeline is compatible with real-time use, i.e. analysis can be done during acquisition. In addition to faster processing, using APR yields memory and storage compression ratios ranging from dozens to thousands depending on the labeling sparsity, saving costs on the storage and computing infrastructures.

Conference Presentation

Citation Download Citation

Jules Scholler, Joel Jonsson, Tomas Jorda-Siquier, Ivana Gantar, Laura Batti, Stephane Pages, Christophe M. Lamy, and Ivo F. Sbalzarini "Open-source image analysis pipeline with 100+ fold speed-up and real-time compression (Conference Presentation)", Proc. SPIE PC12385, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXX, PC1238509 (15 March 2023); https://doi.org/10.1117/12.2647105

ACCESS THE FULL ARTICLE

INSTITUTIONAL
Select your institution to access the SPIE Digital Library.

SELECT YOUR INSTITUTION

PERSONAL
Sign in with your SPIE account to access your personal subscriptions or to use specific features such as save to my library, sign up for alerts, save searches, etc.

PERSONAL SIGN IN

No SPIE Account? Create one

PURCHASE THIS CONTENT

SUBSCRIBE TO DIGITAL LIBRARY

50 downloads per 1-year subscription

Members: $195

Non-members: $335 ADD TO CART

25 downloads per 1 - year subscription

Members: $145

Non-members: $250 ADD TO CART

PURCHASE SINGLE ARTICLE

Includes PDF, HTML & Video, when available