Prebinned tomograms

Big tomograms are difficult to fit in memory. Even if they fit, their visualization can be difficult inside browsers as dtmsice, which load volumetric data in memory. For this reason, it is frequently necessary to keep one or several binned versions of the same tomogram in disk. Some programs in Dynamo can use a prebinned tomogram as a proxy for the full defined tomogram, keeping track of all the coordinate coventions. The most used one is dtmslice. A tomogram with original sidelengths of 4000 x 4000 x 800 pixels will probably make the interaction with dtmslicesluggish and inconvenient. It's more convenient to send to dtmslice a 2 times binned tomogram, with a sidelength of 1000x1000x200 pixels, which can be comfortably navigated. Annotations will be automatically kept in the scale of the original tomogram.

Convention

Naming

The file that represents a prebinend version of another one has to be named:

originalFileName_CatBinnedX.originalFileExtension

where X is the number of times that a binning with bin size 2x2x2 voxels has been applied.

For instance, the 2 times binned version of tomogram.mrc needs to be called tomogram_CatBinned2.mrc

Binning factor

Creation

Through the catalogue

Through dtmslice

Command line

Dedicated tools

Generic tools

Use

In tmslice

Through the catalogue

From the command line

With custom commands