Re: TrakEM question

Posted by Saalfeld, Stephan on Mar 12, 2018; 9:50pm
URL: http://imagej.273.s1.nabble.com/TrakEM-question-tp5020256p5020270.html

Or you build this project into your active Fiji instance:

https://github.com/saalfeldlab/bigdataviewer-trakem2

It will add a plugin

https://github.com/saalfeldlab/bigdataviewer-trakem2/blob/master/src/ma
in/resources/plugins.config

to view the currently open TrakEM2 project with arbitrary reslicing
BigDataViewer.  Without export.

It's a little old and may conflict with other stuff in Fiji, so test in
a fresh copy.

mvn -Dimagej.app.directory=$HOME/packages/Fiji.app clean install

Best,
Stephan

On Mon, 2018-03-12 at 13:53 -0500, Kenneth Sloan wrote:

> Excellent!  Again - thank you.
>
> --
> Kenneth Sloan
> [hidden email]
> Vision is the art of seeing what is invisible to others.
>
>
>
>
>
> >
> > On 12 Mar 2018, at 10:33 , Albert Cardona <[hidden email]>
> > wrote:
> >
> > Hi Kenneth,
> >
> > Glad you find TrakEM2 useful.
> >
> > Internally, TrakEM2 organizes data as a list of 2D planes. Each
> > plane,
> > or section, is modeled by a "Layer" object. The list of Layer
> > instances is the LayerSet.
> >
> > As you point out, your volume is too large for visualization as an
> > orthoslices at 100 % resolution, and you have two parameters to
> > play
> > with: the ROI to restrict to a subvolume, and the magnification.
> >
> > Here is a script that uses both, in jython, and opens an image
> > stack.
> > It requires:
> > 1. That a TrakEM2 project is open.
> > 2. That an ROI is draw using the rectangle tool (optional).
> > 3. Write in the first and last sections (indices, not Z) that you
> > want
> > to include).
> >
> > Will produce 8-bit images. If you want RGB, use ImagePlus.COLOR_RGB
> > in
> > the getFlatImage function. (GRAY16 and GRAY32 won't work.)
> > For 16-bit, use the ExportUnsignedShort.makeFlatImage method
> > instead.
> >
> > If you are intending to visualize the entire volume rather than a
> > small bit, there are alternatives.
> >
> > For one, consider exporting the data as N5
> > (https://github.com/saalfeldlab/n5) and then using the
> > BigDataViewer
> > or the BigCAT to visualize the volume in arbitrary zooms and
> > rotations, as well as orthoslices. With compression, the data would
> > take about 50% of the current storage space.
> >
> > Another option is to view the whole TrakEM2 projevt volume as an
> > ImgLib2 RandomAccessibleInterval (ask Stephan Saalfeld about the
> > script), and then using whatever ImgLib2-based tools you like to
> > crop,
> > process, or visualize, including the BigDataViewer.
> >
> > Yet another option is to export the data for CATMAID (see:
> > https://github.com/axtimwalde/fiji-scripts/blob/master/TrakEM2/catm
> > aid-export2.bsh
> > ).
> >
> > Best,
> >
> > Albert
> >
> >
> > ####################
> > # Export an ImageStack from a range of TrakEM2 layers
> >
> > from ini.trakem2.display import Display, Displayable
> > from ij import ImagePlus, ImageStack
> >
> > # zero-based index:
> > index_first_section = 10
> > index_last_section = 20
> >
> > magnification = 0.25
> >
> > front = Display.getFront()
> > layerset = front.getLayerSet()
> > layers = layerset.getLayers().subList(index_first_section,
> > index_last_section + 1)
> > loader = layerset.getProject().getLoader()
> >
> > # Can be null
> > roi = front.getRoi()
> >
> > # The whole 2D area, or just that of the ROI
> > bounds = roi.getBounds() if roi else layerset.get2DBounds()
> >
> > stack = ImageStack(int(bounds.width * magnification + 0.5),
> >                   int(bounds.height * magnification + 0.5))
> > print stack
> >
> > for layer in layers:
> >  imp = loader.getFlatImage(layer, bounds, magnification, -1,
> > ImagePlus.GRAY8, Displayable, False)
> >  stack.addSlice(imp.getProcessor())
> >
> > ImagePlus("stack", stack).show()
> > ###################
> >
> > 2018-03-10 9:20 GMT-05:00 Kenneth Sloan <[hidden email]>:
> > >
> > > We are using TrakEM to look at a stack of EM images.  It works
> > > great!
> > >
> > > But, we would like to generate orthogonal views of the stack of
> > > images.
> > >
> > > I am, alas, completely ignorant of how TrakEM manages the images
> > > (multiple tiles, multiple slices).
> > >
> > > It seems clear that the image displayed by ImageJ is not a
> > > "stack" as far as ImageJ is concerned.
> > > Any attempt to select that window and apply any Stack command
> > > fails miserably ("must be a stack").
> > > I didn't really think that would work, but I tried it.
> > >
> > > So...is there a way to produce a (perhaps low resolution, perhaps
> > > a limited "brick") stack that can be treated as a normal ImageJ
> > > stack of images, so that we could use (for example) "Orthogonal
> > > Views").
> > >
> > > I expect this will be expensive.  The data set is 10-20TB.  So,
> > > the key is probably "lower resolution or restricted region in
> > > x,y,z"
> > >
> > > --
> > > Kenneth Sloan
> > > [hidden email]
> > > Vision is the art of seeing what is invisible to others.
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> >

--

Stephan Saalfeld, Ph.D.
Group Leader
Janelia Research Campus
19700 Helix Drive | Ashburn, VA 20147
Phone: [phone] | Fax: [phone]
[hidden email]



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