Light-sheet microscopy

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
Description

ASTEC stands for Adaptive Segmentation and Tracking of Embryonic Cells. It proposes a full workflow for time lapse light sheet imaging analysis, including drift/motion compensation before the segmentation itself, and the capacity to correct for it.  It was used to process 3D+t movies acquired by the MuViSPIM light-sheet microscope in particular.

Astec embryon
Description

ClearMap is a toolbox for the analysis and registration of volumetric data from cleared tissues.

It was initially developed to map brain activity at cellular resolution in whole mouse brains using immediate early gene expression. It has since then been extended as a tool for the qunatification of whole mouse brain vascualtur networks at capilary resolution.

It is composed of sevral specialized modules or scripts: tubemap, cellmap, WobblyStitcher.

ClearMap has been designed to analyze O(TB) 3d datasets obtained via light sheet microscopy from iDISCO+ cleared tissue samples immunolabeled for proteins. The ClearMap tools may also be useful for data obtained with other types of microscopes, types of markers, clearing techniques, as well as other species, organs, or samples.

ClearMap SCreenshot
Description

This is the ImageJ/Fiji plugin for StarDist, a cell/nuclei detection method for microscopy images with star-convex shape priors ( typically for Dapi like staining of nuclei). The plugin can be used to apply already trained models to new images.

Stardist
Description

TGMM is a cell tracking solution for large 3D volume (typically lightsheet).

It detects cell nuclei by fitting gaussians on their fluorescent intensity.

It can run on GPU using CUDA and is called via the command line.

has function
need a thumbnail
Description

Web based viewer developped for google for very big data: 

Neuroglancer is a WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons). The segmentation has to be done before loading the dataset, it is not done Inside the viewer.

This is not an official Google product.

It has among other the nice feature of beeing able to generate url for sharing a specific view.

Note that the only supported browser for now are 

  • Chrome >= 51
  • Firefox >= 46

 

Neuroglancer