[Insight-users] Using Bacterial Colonies for segmentation : Morphogenesis Application

[Yasser Bashir]

Great. This works perfectly. Thank you Luis.

Questions regarding visualization of the ITKMesh:

If i set up a pipeline between ITK and VTK and perform the visualization in
VTK, isnt that extremely (un-usably) inefficient?  In general, what is the
most optimum way of viewing an ITKMesh that is forming or deforming over
time.  At this point i am just interested in the wireframe, not the
surfaces.

It would be nice to be able to harness the power of VTK but moving and back
and forth between the UnstructuredGrid and the ITKMesh will incur a HUGE
overhead or so i believe.

Regards.


----- Original Message ----- 
From: "Luis Ibanez" <luis . ibanez at kitware . com>
To: "Yasser Bashir" <itk_at_stanford at yahoo . com>
Cc: <insight-users at itk . org>
Sent: Thursday, December 11, 2003 2:44 PM
Subject: [Insight-users] Using Bacterial Colonies for segmentation :
Morphogenesis Application


>
> Hi Yasser,
>
> Note first that for using the Morphogenesis
> application in 3D you must go to the file
>
>    InsightApplications/Morphogenesis/Cell.h
>
> and change line 41 to be
>
>    Dimension = 3
>
> instead of
>
>    Dimension = 2
>
>
> ---
>
> Also, the Morphogenesis application requires you
> to write two small text files with parameters.
>
> This is far from being an ideal interface...
> but it is the way it is working right now...
>
>
> So,
> please write text files with names
>
>     CellularAggregate.dat
>     GradientEatingBacteria.dat
>
>
> In the file CellularAggregate.dat you put
> values defining the X,Y,Z coordinates of
> the first egg cell.
>
> This is plain ascii text just like
>
>           124  34  68
>
> where those values are in millimeters
> (e.g.  physical units of your image,
> not pixel units).  [ This should be replaced
> with an interactive  mouse click... whenever
> we got time to work further in this application...]
>
>
> In the file GradientEatingBacteria.dat you
> put values
>
> 1) Default cell radius
> 2) Growth radius increment
> 3) Growth radius limit
> 4) Chemo attractant low value
> 5) Chemo attractant high value
>
> The meaning of these values is:
>
> 1) the size in millimeters of the
>     cell at birth time. A typical
>     value is 2.5
>
> 2) how much the cell grows at each
>     iteration. A typical value is 0.1
>
> 3) The adult size radius of the
>     bacterial cell. A typical value is
>     5.0.  This values defines how
>     coarse the mesh of the cellular
>     colony will be by the end of the
>     segmentation.
>
> 4 & 5) are threshold values of gray
>     levels from your image.
>     The bacteria will grow and reproduce
>     happily in the regions of the image
>     having gray level values in the range
>     defined by these two values.
>
> So, a typical file will look like
>
> 2.5
> 0.1
> 5.0
> 120
> 180
>
> For filling in a region with gray level
> intensities in the range [120:180].
>
>
> Put these two files in the directory
> from which you are executing the Morphogenesis
> executable.
>
>
> When you run the executable, do the following:
>
>
> 1) Load your dataset using the option
>     "Load Substrate", give it a string name,
>     and click on the option "make visible".
>
>     You can zoom in/out by using Ctrl+rightmousebutton
>     and dragging.
>
> 2) Go to the "View" menu and select "Species",
>     the smarter bacteria at this point is the
>     "Gradient Eating Bacteria", select this species
>     and click on "Create Egg".
>
>     At this point a sphere should appear on the
>     3D view.
>
> 3) then click on the "play" button. The one with
>     the black triangular label. The bacteria should
>     start growing and reproducing filling in the
>     region of the image defined by the two threshold.
>
>     Make sure that the initial position of the egg
>     cell is in a region with gray values in the
>     range defined by the two threshold values.
>
>
>     You can stop the activity of the bacterial colony
>     by clicking on the "stop" button. (the black square).
>
>     Note that the method will never stop by itself.
>     Bacteria will keep trying to reproduce. You simply
>     stop it when you judge that no new cells are being
>     born (a cell counter is in the interface)
>     [This could also be easily fixed by setting a timeout
>      for the next cellular division. E.g. stop the colony
>      if no cells are divided in a period of 3 seconds]
>
>
>
> Please let us know if you have any further question.
>
>
>    Thanks
>
>
>
>       Luis
>
>
>
>
> -------------------------
> Yasser Bashir wrote:
>
> > Thank you Luis.
> .
> >
> > I have a question regarding the Morphogenesis application. Can you
> please
> > tell me how can i generate a bacterial colony inside my 3D image.  It
> seems
> > to work fine for 2D slices but when i load my segmented 3D image and
> try
> > generating the bacterial colony, nothing happens i.e. im unable to
> see the
> > bacterial colony grow.
> >
> > Regards
> >
> > yasser.
> >
> >
> >
> >
>
>
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