Difference between revisions of "Viewing tomograms"

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(Tomogram browsers)
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== Tomogram browsers==
 
== Tomogram browsers==
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Most browsers can be invoked directly from the command line or from a GUI linked to a catalogue.
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* <tt>dtmshow</tt> quick, simple browsing outside of the catalogue system
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* <tt>dpreview</tt> quick inspection of a few slides of catalogued volumes, for sending areas to other browser
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* <tt>dtmview</tt> annotation of isolated particles and membranes inside the catalogue system
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* <tt>dtmslice</tt> annotation of filaments and membranes inside the catalogue system
  
 
=== <tt>dtmshow</tt> ===
 
=== <tt>dtmshow</tt> ===
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Sliding montages of areas inside a tomogram are specially useful for modelling membranes. Sliding montages are connected with the [[model pool]] and provide semiautomatic tools to track points manually picked in one level on the following levels.
 
Sliding montages of areas inside a tomogram are specially useful for modelling membranes. Sliding montages are connected with the [[model pool]] and provide semiautomatic tools to track points manually picked in one level on the following levels.
 
 
  
 
== Binned tomograms ==  
 
== Binned tomograms ==  

Revision as of 17:06, 18 March 2016

Dynamo offers several ways to visualize tomograms. The choice of one or other program depends on varios factors, like "How big is the tomogram?" "Are you going to annotate models on them?".

Tomogram browsers

Most browsers can be invoked directly from the command line or from a GUI linked to a catalogue.


  • dtmshow quick, simple browsing outside of the catalogue system
  • dpreview quick inspection of a few slides of catalogued volumes, for sending areas to other browser
  • dtmview annotation of isolated particles and membranes inside the catalogue system
  • dtmslice annotation of filaments and membranes inside the catalogue system

dtmshow

The simplest visualization system is the program dtmshow, callable from the command line and linked by many Dynamo GUIs. It's a lightweight slice-based browser. The user can choose to use it by preloading of the full tomogram or by accessing the disk for each depicted slice ("on-the-fly" modus). dtmshowDoes not allow to make complex annotations, or to register them inside the Catalogue via the model pool

dpreview

A screenshot on dpreview

dpreview goes a step further than dtmshow. It is connected with the Catalogue system, in fact 'open with dpreview' is one of the main options that you get when selecting a catalogued tomogram in the dcm GUI.

In dpreviewslices are always accessed "on the fly", so that browsing can be slow (especially if trying to depict slices orthogonal to the x- or y- directions, which demand multiple I/O operations to gather a slice whose pixels are scattered in the disk). The main function of the dpreview is to provide a "preview" of the disk contents of a tomogram, letting the user to specify and area of the tomogram and a binning level. This fragment will be read into memory and passed to dtmview or dtslice


dtmview

Is normally invoked by the dcm GUI or by dpreview . It is oriented to show concurrently slices representing orthogonal cuts inside a volume with a high level of control of the number of depicted slices.

The main utility of dtmview is for clicking sets of isolated particles.


dtslicer

Is normally invoked by the dcm GUI or by dpreview . It depicts in 3d a slide or arbitrary orientation that can be moved freely inside the tomogram. This is a suitable browser for filament geometries. It is also suitable to locate the extent of membranes a send them over to the Sliding Montage browser for annotation.


Sliding montage

Sliding montage generated fromdtslice

A sliding montage presents simultaneously a selection of slides of the tomogram. The user can choose to distance between consecutively depicted slices, and navigate inside the tomogram.

Sliding montages of areas inside a tomogram are specially useful for modelling membranes. Sliding montages are connected with the model pool and provide semiautomatic tools to track points manually picked in one level on the following levels.

Binned tomograms

Prebinned tomograms

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