[ImageJ-devel] Using ImgLib2 with JavaFX and other questions.

[Tobias Pietzsch]

Hi Michael,

On 29 Aug 2014, at 13:09, Michael Ellis <michael.ellis at dsuk.biz> wrote:

> I am trying to learn about ImgLib2
> 
> In particular I could do with help for the following:
> 
> All my images will be 2D byte images typically of size 1300x1000.
> 
> How do I get an Img into a format compatible for displaying within JavaFX (rather than using ImageJFunctions.show() )?
> Assuming there is no explicit JavaFX support in ImgLib2, I think this boils down to producing and 24 bit RGB or 32bit ARGB image where I can access the data. But how do I do this?

Have a look at ARGBScreenImage which extends ArrayImg< ARGBType, IntArray >.
This s a 2D image intended for displaying on screen. You can get to the underlying 32bit ARGB int[] array by
	public int[] getData()
or get it wrapped in a AWT BufferedImage by
	public BufferedImage image()

> 
> How would I combine multiple 2D 8 bit image planes (up to 7 planes, each with own colour table) and combine them under programatic control into a single RGB image where every pixel in the destination image dest[x, y] is a function of the pixels at src[plane, x, y]?

See
net.imglib2.display.projector.composite.CompositeXYProjector
or 
net.imglib2.display.projector.composite.CompositeXYRandomAccessibleProjector
They should do exactly what you need. Note, that they expect that [x, y] of your image to composite are the first two dimensions. So it would work with [x, y, …, plane, …].
If you really have [plane, x, y], you can use Views.permute(...) to get a virtual view into your data as [x, y, plane].

> 
> How would I  threshold a 2D Img producing a 1 bit Img?

You could simply do this by implementing a Converter< __YourImageType__, BitType > and then using Converters.convert(...) to get a virtual view into your data as a thresholded  1 bit image.

> How would I fill holes in the binary thresholded Img?

Have a look through imglib2-algorithms, imglib2-algorithms, and imglib2-ops. There should be something there.

> How could I identify and label objects in the binary thresholded Img and extract a concise description of the object boundaries (e.g. polygon, or chain code descriptions)?

To identify objects you could use
net.imglib2.algorithm.labeling.AllConnectedComponents
About the object descriptions, I don’t think we have anything for that, but I’m not sure. Maybe someone familiar with imglib2-ops can comment?

best regards,
Tobias

> 
> How can I register a multiple  Imgs using cross correlation image registration?
> 
> Any help would be appreciated. I’m not looking for complete solutions to this and whilst this work is intended for a commercial product, I am happy to contribute all the source code examples I generate by way of investigating any of the above.
> 
> — Michael Ellis
> Digital Scientific UK Ltd.
> 
> 
> 
> 
> 
> 
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