Synonyms
LSFM
Digitally scanned Lightsheet Microscopy
Selective Plane Illumination Microscopy
Light-sheet fluorescence microscopy
DSLM
SPIM
Lattice Light-sheet Microscopy
Dual-View inverted SPIM
Spherical aberrations assisted Extended Depth-of-field Lightsheet Microscopy
Bessel Beam Lightsheet Microscopy
single objective Selective Plane Illumination Microscopy
Hardware implementations: multidirectional SPIM
LLSM
Clarity Optimized Lightsheet Microscopy
Multiview Selective Plane Illumination Microscopy
MuViSPIM
inverted SPIM
soSPIM
diSPIM
COLM
SPED
mSPIM
iSPIM

Microscope autopilot

Description

AutoPilot is the open source project that hosts the general algorithm for fast and robust assessment of local image quality, an automated computational method for image-based mapping of the three-dimensional light-sheet geometry inside a fluorescently labeled biological specimen, and a general algorithm for data-driven optimization of the system state of light-sheet microscopes capable of multi-color imaging with multiple illumination and detection arms.

has function

CSBDeep, a toolbox for Content-aware Image Restoration (CARE) in Knime

Description

Deep learning based restoration, with guidelines for training. See also the Fiji plugin.

CSBDeep, a toolbox for Content-aware Image Restoration (CARE) in Fiji

Description

Deep learning for fluorescence image restoration (denoising, deconvolution). Requires training on your data set but the procedure is described.

CARE

MaMuT

Description

MaMuT is an end user plugin that combines the BigDataViewer and TrackMate to provide an application that allow browsing, annotating and curating annotations for large image data.

Spark Stitcher

Description

Reconstruct big images from overlapping tiled images on a Spark cluster.

The code is based on the Stitching plugin for Fiji https://github.com/fiji/Stitching

SparkStitching

VMTK: Vascular Modeling Toolkit

Description

vmtk is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

vmtk is composed of

  • C++ classes (VTK and ITK -based algorithms)
  • Python classes (high-level functionality - each class is a script)
  • PypeS - Python pipeable scripts, a framework which enables vmtk scripts to interact with each other

 

ClearVolume

Description

ClearVolume is a real-time live 3D visualization library designed for high-end volumetric microscopes such as SPIM and DLSM microscopes. With ClearVolume you can see live on your screen the stacks acquired by your microscope instead of waiting for offline post-processing to give you an intuitive and comprehensive view on your data. The biologists can immediately decide whether a sample is worth imaging. ClearVolume can easily be integrated into existing Java, C/C++, Python, or LabVIEW based microscope software. It has a dedicated interface to MicroManager/OpenSpim/OpenSpin control software. ClearVolume supports multi-channels, live 3D data streaming from remote microscopes, and uses a multi-pass Fibonacci rendering algorithm that can handle large volumes. Moreover, ClearVolume is integrated into the Fiji/ImageJ2/KNIME ecosystem. You can now open your stacks with ClearVolume from within these popular frameworks for offline viewing.

has function

Multiview Reconstruction

Description

The Multiview Reconstruction software package enables users to register, fuse, deconvolve and view multiview microscopy images. The software is designed for lightsheet fluorescence microscopy (LSFM), but is applicable to any form of three or higher dimensional imaging modalities like confocal timeseries or multicolor stacks. 

need a thumbnail

BigDataViewer

Description

The BigDataViewer is a re-slicing browser for terabyte-sized multi-view image sequences. BigDataViewer was developed with multi-view light-sheet microscopy data in mind and integrates well with Fiji's SPIMage processing pipeline.