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Selective plane illumination microscopy software tools

Selective Plane Illumination Microscopy (SPIM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via…
BDV
Desktop

BDV BigDataViewer

A re-slicing browser for terabyte-sized multi-view image sequences.…

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…

OpenSPIM
Desktop

OpenSPIM

An open hardware and software platform for constructing a customizable…

An open hardware and software platform for constructing a customizable microscope for selective-plane illumination microscopy (SPIM). The OpenSPIM platform is shared with the scientific community…

OpenSegSPIM
Desktop

OpenSegSPIM

An open access and user friendly 3D automatic quantitative analysis tool for…

An open access and user friendly 3D automatic quantitative analysis tool for single plane illumination microscopy (SPIM) data. OpenSegSPIM is designed to extract quantitative relevant information…

snakemake…
Desktop

snakemake workflows

An automated workflow for processing large multiview, multi-channel,…

An automated workflow for processing large multiview, multi-channel, multi-illumination time-lapse selective plane illumination microscopy (SPIM) data on a single workstation or in parallel on a HPC…

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