Difference between revisions of "Prebinned tomograms"

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=== Through the catalogue ===
=== Through the catalogue ===
The Catalogue GUI  
The [[dcm GUI| catalogue GUI]]
[[File:PrebinningCatalogueMenu.png|thumb|center|500px|A tomogram with several vesicles shown in <tt>dtmslice</tt>]]
=== Through dtmslice ===
=== Through dtmslice ===

Revision as of 18:08, 23 February 2017

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.

Storage of prebinned tomograms is normally not problematic in terms of disk space: a 2x binned tomogram has 64 times less voxels than the original one.



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


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

needs to be called 

Both tomograms need to reside in the same directory in order to let Dynamo find the prebinned version of the respective tomogram file.

Binning factor

The binning factor expresses the number of single binnings operated on one tomogram consecutively. Each binning represents the collapse of a cube of 2x2x2 voxels of the original file into a single voxel of the prebinned file. If the original tomogram had a sidelength of L voxels along one dimension, the 1x binned tomogram will have L/2 voxels, the 2x binned one will have L/4, etc.


Binning tomograms can be a time intensive procedure. The attempt of reading a full resolution tomogram into memory in one step can easily block the computer. Binning programs in Dynamo will proceed by loading into memory only small slabs (i.e., sets of correlative z-slices) of the original volume, binning the slab and then writing the slab into a file representing the binned file. If the slab size is too small, the process can be rather long. If the slab size is too large, you risk crowding the memory. If the binning procedure is performed with many processors, each one will read a different slab in parallel, so that you need to take into account the total memory use in a given time.

We default slab size is 50, which uses to work reasonably in most occasions. The different methods to prebin the tomograms will provide different levels of control on the way the binning is computed.

Through the catalogue

The catalogue GUI

A tomogram with several vesicles shown in dtmslice

Through dtmslice

When you open a tomogram with dtmslice, you can ask to open the prebinned version:

dtmslice myTomogram.mrc -pb 2 -c myCatalogue

will open a prebinned version of the tomogram myTomogram.mrc. If the file myTomogram_CatBinned2.mrc does not exist, it will be created on the fly. The other flag, -c myCatalogue is merely to declare in which catalogue we are opening the tomogram, i.e., where the models that we create during this session will be created.

During the creation of prebinned tomograms, a slabsize of 50 is used by default.

Command line

Dedicated tools

Generic tools


In tmslice

Through the catalogue

From the command line

With custom commands