Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Nov;21(11):1967-1969.
doi: 10.1038/s41592-024-02413-4.

Navigate: an open-source platform for smart light-sheet microscopy

Zach Marin #  1   2 , Xiaoding Wang #  1 , Dax W Collison  1 , Conor McFadden  1 , Jinlong Lin  1 , Hazel M Borges  1 , Bingying Chen  1 , Dushyant Mehra  1 , Qionghua Shen  1 , Seweryn Gałecki  1   3 , Stephan Daetwyler  1 , Steven J Sheppard  4 , Phu Thien  4 , Baylee A Porter  5 , Suzanne D Conzen  5 , Douglas P Shepherd  4 , Reto Fiolka  1 , Kevin M Dean  6   7
Affiliations

Navigate: an open-source platform for smart light-sheet microscopy

Zach Marin et al. Nat Methods. 2024 Nov.
No abstract available

PubMed Disclaimer

Figures

Figure 1:
Figure 1:
navigate provides a GUI with access to reconfigurable smart acquisition pipelines and runs on multiple types of light-sheet configurations. a, Screenshot of the navigate GUI running a mesoSPIM with GUI controls for the smart acquisition routine diagrammed in b. The blue dashed boxes show the Feature menu, where the controls are accessed, and the corresponding editor for the smart routine. The red dashed boxes show a decision node and the corresponding editor for this decision node. b, An example of a reconfigurable, decision-based pipeline that acquires a Z-Stack if tissue is present at a particular stage position. The user guide in the Supplementary Documentation features a tutorial on how to build this pipeline. Individual features can be swapped for other features that ship with the software or with custom-built plugin features. c, navigate can integrate advanced optical techniques, such as adaptive optics. (Left) An iterative sensorless adaptive optics scheme uses the Discrete Cosine Transform Shannon (DCTS) Entropy to estimate aberrations. Inset shows the final actuator positions of the deformable mirror. (Middle) Final estimated adaptive optics wavefront. (Right) 3D stack of a ventricle within the vasculature of a zebrafish embryo (labelled with kdrl:eGFP), before and after adaptive optics. d, Example image of an expanded mouse lung, captured with an upright ctASLM using navigate. e, Results of smart imaging workflow from a and b, captured on a mesoSPIM. Bone tissue imaged at 1x magnification (left) was automatically segmented and tiled at 6x magnification (right). Imaged regions, indicated by dashed white boxes, were saved to BDV and displayed in a tiled format.
See this image and copyright information in PMC

Update of

References

    1. McDole K. et al. In Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single-Cell Level. Cell 175, 859–876 e833 (2018). 10.1016/j.cell.2018.09.031 - DOI - PubMed
    1. Mahecic D. et al. Event-driven acquisition for content-enriched microscopy. Nat Methods 19, 1262–1267 (2022). 10.1038/s41592-022-01589-x - DOI - PMC - PubMed
    1. Shi Y. et al. Smart lattice light-sheet microscopy for imaging rare and complex cellular events. Nat Methods (2024). 10.1038/s41592-023-02126-0 - DOI - PMC - PubMed
    1. Conrad C. et al. Micropilot: automation of fluorescence microscopy-based imaging for systems biology. Nat Methods 8, 246–249 (2011). 10.1038/nmeth.1558 - DOI - PMC - PubMed
    1. Alvelid J, Damenti M, Sgattoni C & Testa I Event-triggered STED imaging. Nat Methods 19, 1268–1275 (2022). 10.1038/s41592-022-01588-y - DOI - PMC - PubMed

LinkOut - more resources