llsm

llsm is a set of Scala libraries for preprocessing and conversion of raw data from early implementations of the Lattice Light-sheet Microscope¹.

Features include:

• Read and parse LLSM metadata from raw LLSM data from the Janelia LabView application.
• Read LLSM raw data from the Janelia LabView application.
• Deskew LLSM volumes.
• Output LLSM volumes as OME-TIFF or BigDataViewer HDF5 formats.

llsm is underpinned by Typelevel and ImageJ/Fiji community libraries including cats, imglib2 and scifio.

Note: Please be aware that these libraries are still in heavy development and are likely to change substantially.

¹Chen, B.-C., Legant, W. R., Wang, K., Shao, L., Milkie, D. E., Davidson, M. W., et al. (2014). Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science (New York, N.Y.), 346(6208), 1257998–1257998. http://doi.org/10.1126/science.1257998

Acknowledgements

llsm forms part of the Australian National Data Service (ANDS) Trusted Lattice Light-Sheet Microscopy data project. This project is a collaboration between:

• Monash University
• University of New South Wales
• University of Queensland

Development of llsm is supported by:

• Australian National Data Service (ANDS)
• Nectar

License

This code is licensed under the MIT license.