lightsheet

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

navigate - open source light-sheet microscope controls

Archived: control, reconstruction, and analysis code for oblique plane microscopy.

An open-source tool for characterizing PSF and FWHM measurements from light-microscopic 2D and 3D images of microspheres.

shrimPy: Smart High-throughput Robust Imaging & Measurement in Python

Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.

Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

#ZVQ - Zebrafish Vascular Quantification - https://doi.org/10.1242/dev.199720

SnakeBIDS app for quantitative analysis of SPIM (lightsheet) brain data

GUI and code for controlling an oblique plane microscope with projection imaging, sensorless adaptive optics, and integrated microfluidics.

MATLAB tools for handling mesoSPIM data

Lazy loader napari plugin for mesoSPIM datasets

A integrated analysis toolbox for 3D spatial transcriptome, enables highly accurate 3D registration for large volume images, and provides barcoding and decoding analysis for spatial transcriptome of thick tissue.

MAXWELL: A tandem use X-ray/visible light microscopy technique at BL29XU of the RIKEN SPring-8 Center, Japan.

Image acquisition software for mesoSPIM light-sheet microscopes.