> 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/catmaid-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>
>
>
> --
>
http://albert.rierol.net>
http://www.janelia.org/lab/cardona-lab>
https://www.pdn.cam.ac.uk/directory/albert-cardona>
> --
> ImageJ mailing list:
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