Software

The first step is acquiring the image data, then the images must be manipulated to give the information the experimenter needs.

Data acquisition can be performed using the ASIdiSPIM plugin in Micro-Manager, using custom-written LabView programs, or using other software that is not yet documented on this wiki (both commercial or home-built). The acquisition software will produce image files.

To combining the two views of diSPIM data into a single dataset with isotropic resolution requires registering the two views and then intelligently merging them. There are two open-source programs for doing that, MIPAV GenerateFusion and the Fiji Multi-view Reconstruction plugin. The former was created at NIH in close collaboration with the Shroff group. The second was originally developed for the OpenSPIM community but can be applied to diSPIM data as well. Improving the data analysis of light sheet data is an area of active development by multiple academic groups. Hopefully companies that sell image analysis software will add registration/fusion ability to their offerings.

Further analysis is often required depending on the experiment, for instance doing automated cell tracking over a time-series or stitching together 3D volumes into a 3D volume larger than can be acquired in one pass.

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