Difference between revisions of "Viewing tomograms"

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''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?".
 
''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?".
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== Tomogram browsers==
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=== <tt>dtmshow</tt> ===
  
 
The simplest visualization system is the program <tt>dtmshow</tt>, 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). <tt>dtmshow</tt>Does not allow to make complex annotations, or to register them inside the [[Catalogue]] via the [[model pool]]
 
The simplest visualization system is the program <tt>dtmshow</tt>, 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). <tt>dtmshow</tt>Does not allow to make complex annotations, or to register them inside the [[Catalogue]] via the [[model pool]]
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=== dpreview ===
  
 
<tt>dpreview</tt> goes a step further that <tt>dtmshow</tt>. It is connected with the [[Catalogue]] system, in fact 'open with <tt>dpreview</tt>' is one of the main options that you get when selecting a catalogued tomogram in the [[dcm GUI]].   
 
<tt>dpreview</tt> goes a step further that <tt>dtmshow</tt>. It is connected with the [[Catalogue]] system, in fact 'open with <tt>dpreview</tt>' is one of the main options that you get when selecting a catalogued tomogram in the [[dcm GUI]].   
  
 
In <tt>dpreview</tt>slices 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).
 
In <tt>dpreview</tt>slices 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 <tt>dpreview</tt> is to provide a "preview" of the disk contents of a tomogram, letting the user to specify and area of the tomogram  
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The main function of the <tt>dpreview</tt> 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 <tt>dtmview</tt> or <tt>dtslice</tt>
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===<tt>dtmview</tt> ===
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Is normally invoked by the [[dcm GUI]] or by <tt>dpreview</tt> . 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.
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The main utility of <tt>dtmview</tt> is for clicking sets of isolated particles. 
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===<tt>dtslice</tt>===
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Is normally invoked by the [[dcm GUI]] or by <tt>dpreview</tt> . 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.
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===Sliding montage===
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Sliding montages of areas inside a tomogram are
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== Binned tomograms ==
  
<tt>dtmview</tt>
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=== Prebinned tomograms ===
  
<tt>dtslice</tt> allows
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===

Revision as of 14:59, 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

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

dpreview goes a step further that 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.


dtslice

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 montages of areas inside a tomogram are


Binned tomograms

Prebinned tomograms

=