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

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
Description

Automated workflow for performing multiview reconstruction of large multiview, multichannel, multiillumination time-lapse SPIM data on a high performance computing (HPC) cluster or on a single workstation.