View source for Walkthrough on manual marker clicking

Reconstruction of a tomogram implies the availability of a set of alignment parameters that bring the tilt series delivered by the microscopio onto a compatible reference.
Fiducial markers can be located using automated methods. In this walkthrough, we describe the tools that ''Dynamo'' offers to locate them ''manually'' through graphical  interaction with the tilt series.

= Data set =

We suggest to follow this tutorial withthe  data set from  the public EMPIAR database (entry number 10064, data item VPP_tomo4.mrc), which can be accessed through an ftp server:

 <tt>get ftp://ftp.ebi.ac.uk/pub/databases/empiar/archive/10064/data/VPP_tomo4.mrc</tt>

in linux, or, in Mac:

 <tt>curl -O  ftp://ftp.ebi.ac.uk/pub/databases/empiar/archive/10064/data/VPP_tomo4.mrc</tt>

= The <tt>dmarkers</tt> GUI =

This GUI is the basic tool for exploring tilt series and annotating on it  using  ''Dynamo''. It allows to edit manually positions of markers, to fit them to a projection model, and to create an aligned data stack and a reconstruction based on this fitting.

== Loading the data ==

Opening the <tt>dmarkers</tt> GUI on a tilt series:

It is convenient to first read the tilt series:

 <tt>ts = dread('VPP_tomo4.mrc');</tt>

and then pass the variable to the gui <tt>dmarkers</tt>:

 <tt> gui = dmarkers('riboVpp.mrc','tiltAngles',-60:2:60);</tt>

here, <tt>gui</tt> is just a handle to the GUI. This handle can be used on a later point to operate on it. Note that we also need to pass the tilt angles, as they will be needed for fitting a projection model. 

[[File:ManualAlignmentDmarkers.png|thumb|center|600px| <tt>dmarkers</tt> GUI ]]

== Basic visualization controls ==

=== Slide on micrographs ===
* Use the slide bar to view a transition of the micrographs (lower resolution images will be shown during the transition, full resolution images will be shown )
* left and right arrows move the  previous or next micrograph in the tilt series.

===Zoom=== 
* You can zoom into a point by using the wheel. 
* The small red  window in the tool bar can be used as magnifying-glass to zoom in into a  hand-draw a region.
* The tool with the four arrows pointing into the corners zooms out of the scene totally.

[[File:ManualAlignmentControls.png|thumb|center|400px|  Basic controls inn <tt>dmarkers</tt> GUI ]]

=== Dragging ===
The scene gets dragged by moving the mouse while keeping pressed the primary mouse button.

=== Elimination of defective tilts ===

Some micrographs may be defective because of errors during acquisition. They can be markers as invalid by the key  <tt>x</tt>. If you want to undo the marking of a micrograph as invalid, use <tt>shift+x</tt>.

== Initiating a trace ==
A  three-dimensional gold bead is represented by a ''trace''. A trace is a set of ''observations'', where we call observation to the location of the projection of a gold bead in a given micrograph.

The tool with a black point and a red edge starts the trace initiator. The cursor in the GUI becomes a cross; while this cursor is active, clicking on the screen will create a new gold bead.

== Following a trace ==
To select a gold bead, click on it with the mouse, a green box will appear on the observation corresponding to the selected markers  in the current micrograph. '''Important'''  to add observations into a trace that you have just created, you need to select it, otherwise your next clicks on the screen will be assigned to the trace that is currently under selection.

Once you have selected a gold bead, you should switch off the tool for adding gold beads, and switch on the tool for adding observations to the gold bead currently under selection. The icon represents a point being tracked  across  several micrographs.

You can use the arrows to move to the next or previous micrograph after clicking the gold bead.

Additionally, you can connect the ''click and right'' or ''click and left'' tools. When they are switched on, after a click on the screen, the GUI will automatically move to the next micrograph.

[[File:ManualAlignmentSetGoldBead.png |thumb|center|400px|  The gold bead click tools sets new traces, the track tool allows adding new observations to the currently selected trace ]]

=== Key controls during clicking ===

* <tt>d</tt> will delete the closest observation (point in currently shown  micrograph).
* <tt>shift</tt> + <tt>d</tt> will delete a full trace.
*  <tt>m</tt> will move the observation of the currently selected shape to the location of the cursor.

=== Auxiliar views during clicking ===
There are two auxiliary GUIs that can be used to control the growth of the traces based as you click the points. The ''occupancy'' window updates as a new observation is added into a gold bead, showing the current content of each trace. And additional control shows the content of each trace as new points are clicked inside.

[[File:ManualAlignmentControlViewers.png |thumb|center|400px|  Tools to follow the traces across the micrographs ]]

= Fitting to an alignment model =

When you have enough observations, you can proceed to fitting the location of your gold beads to a projection model. The tool with the icon <tt>Fit</tt> will compute a set of shifts and a single angle <tt>psi</tt> of rotation for the tilt axis. 

In the ''Fit'' menu on the GUI, you can find the current error, i.e., the mean residual between each observation and the projection estimated by the fitting model.

[[File:ManualAlignmentFitting.png |thumb|center|400px| Fitting menu in <tt>dmarkers</tt>]]

== Extended fitting models ==
In a coarse fitting, ''Dynamo'' only tries to solve for shifts and a single rotation angle for all micrographs. It is possible to refine this fitting allowing a different rotation of the tilt axis for each micrograph. You can select for a richer model that computes for one different rotation angle on each micrograph by checking the option <tt>eachTilt</tt>  on the parameter <tt>psi</tt> (default is <tt>single</tt>). 

Although you will get a lower error value, this might be due to overfitting. Thus, richer parametric models should not be used if you don't have enough markers on each micrograph (in the order of the tens.)

= The reconstruction GUI = 
Once you have clicked on your markers, and you have fitted them to an alignment model, you can proceed to compute a reconstruction. The <tt>[Reconstruction]</tt> tab in <tt>dmarkers</tt> opens an external GUI that uses the fitting model computed in <tt>dmarkers</tt> to create an aligned version of the tilt series and then a reconstruction.

[[File:ManualAlignmentReconstructorGUI.png |thumb|center|600px| Reconstruction GUI spawn by <tt>dmarkers</tt>]]

This GUI can be followed on a step by step basis. Completed steps will be shown in bold. Results produced by the computing step can be visualized through secondary-clicking of each view panel.

The task in the workshop ''ends''' with the completion of two binned reconstructions, one reconstructed through SIRT-like filtering, and another one reconstructed by WBP.  The SIRT-like reconstruction exhibits a higher contrast, and it's frequently used for particle picking.  The WBP reconstruction conserves its high frequencies, and it's the one we should use for subtomogram averaging.

[[File:ManualAlignmentSIRTWBP.png |thumb|center|800px| Sirt-like and WBP reconstruction]]

= Reconstruction through the command line =

Creating reconstructions through the command line is convenient when organizing the processing of  batches of tilt series. Automatic selection of markers is explored in a different walkthrough, here we describe the command line tools for creating reconstructions once a marker set is available. The steps are:
* Fitting of the available markers (using a ''fitter'' object).
* Extraction of alignment  parameters (using an ''aligner'' object).
* Creation of an aligned tilt series.
* Weighting the tilt series appropriately for a weighted-back-projection or Sirt-like reconstruction.
* Creation of the tomogram through back projecting the filtered aligned stack.

If you have a set of markers saved  in a file in disk, you can load it to memory through:

 <tt>markers = dread('Tracks.dms');</tt>

Then, you can create a fitter object:

 <tt>fitter = dfitter(markers);</tt>
 
This object needs to know where to put the rotation center of the aligned tilt series. 
 <tt>fitter.setCenter(ts);</tt>

and prepare it to run with standard parameters:

 <tt>fitter.physical.defaultInitialization();</tt>

The command

 <tt>fitter.linearScan();</tt>

will then compute the best <tt>psi</tt> angle for the rotation of the tilt axis together with the shifts.  They can be gathered into an stack alignment object

 <tt>stackAligner = fitter.getStackAligner();</tt>

that gets then applied onto the original tilt series in the variable <tt>ts</tt>.

 <tt>tsAligned  = stackAligner.applyOnStack(ts);</tt> 

This aligned stack can be visualized through:

 <tt>dtmshow(tsAligned);</tt>

== Binned reconstruction  ==

A reconstruction with a bigger pixel size can be computed by resizing both tilt series and markers. A marker object can be resized through:

 <tt>markersBinned = markers.math.bin(2);</tt>

Here, the factor 2 indicates that the coordinates of the markers get halved twice. This factor needs to be applied also to the tilt series:

 <tt>tsBinned = dpktilt.bin(ts,2);</tt>.

Now, we can refit the binned markers, proceeding as above:

 <pre>binnedFitter = dfitter(markersBinned);</tt>
binnedFitter.setCenter(tsBinned);
binnedFitter.defaultInitialization();
binnedFitter.linearScan();
binnedAligner = binnedFitter.getStackAligner();
tsBinnedAligned = binnedAligner.applyOnStack(tsBinned);</pre>

To create a weighted back projection reconstruction, this stack needs to be weighted with a ramp function in the Fourier space.
 
 <tt> tsBinnedRamp = dpktomo.rec.applyRampFilter(tsBinnedAligned);</tt>

Then, we can use the command <tt>dpktilt.math.backproject</tt> to create a reconstruction.

  <tt>fbp = dpktilt.math.backproject([600,600,600],tsBinnedRamp,-60:2:60,'mw','*'); </tt>.

Here, the flag <tt>'mw'</tt> is merely instructing ''Dynamo'' to use all available cores.

The reconstruction object <tt>fbp</tt> contains the reconstructed tomogram in its property <tt>.rec</tt>, which can be visualized through:
 
 <tt>dtmshow(fpp.rec);</tt>