bioRxivBiophysics
navigate: an open-source platform for smart light-sheet microscopy.
Z. Marin, X. Wang, D. W. Collison, C. McFadden, J. Lin, H. Borges, B. Chen, D. Mehra, Q. Shen, S. Galecki, S. Daetwyler, R. P. Fiolka, K. M. Dean
Abstract
navigate is a turnkey, open-source software solution designed to enhance light-sheet fluorescence microscopy (LSFM) by integrating smart microscopy techniques into a user-friendly framework. It enables automated, intelligent imaging with a Python-based control system that supports GUI-reconfigurable acquisition routines and the integration of diverse hardware sets. As a comprehensive package, navigate democratizes access to advanced LSFM capabilities, facilitating the development and implementation of smart microscopy workflows without requiring deep programming knowledge or specialized expertise in light-sheet microscopy.
- assay: imaging
- assay: fluorescence / live-cell microscopy
- research focus: software / tool
- research focus: benchmarking
- approach: experimental assay
- approach: wet-lab / biochemical assay
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- The mesoSPIM initiative: open-source light-sheet mesoscopes for imaging in cleared tissue
Fabian F. Voigt, Daniel S. Kirschenbaum, … Fritjof Helmchen·bioRxiv·Mar 18, 2019
- Multi-immersion Oblique Plane Microscope (miOPM): A reconfigurable platform for high-resolution Light-Sheet Fluorescence Microscopy.
Bingying Chen, Alfred Millett-Sikking, … Reto Paul Fiolka·bioRxiv·Oct 4, 2025
- descSPIM: Affordable and Easy-to-Build Light-Sheet Microscopy for Tissue Clearing Technique Users
K. Otomo, T. Omura, … E. A. Susaki·bioRxiv·May 2, 2023
- Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science
M. A. Phillips, D. M. Susano Pinto, … I. M. Dobbie·bioRxiv·Jan 18, 2021
- Micro-Magellan: A flexible, open source acquisition software for high throughput biological light microscopy
Henry Pinkard, Nico Stuurman, … Matthew F Krummel·bioRxiv·Jan 28, 2016
- Light sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development
Johannes Girstmair, Anne Zakrzewski, … Maximilian J Telford·BMC Developmental BiologyPeer-reviewed·Jun 30, 2016