[SCIFIO] Fiji Plugin Almost Finished

[Curtis Rueden]

Hi Ajeet,

[CCing scifio mailing list, which is the best place to discuss these sorts
of file format issues.]

> Johannes, I have a tiff image stack of images all of different width and
> height. When reading with the bioformats importer, it assumes that all
> images are the same size and sets the width/height for all images to
> that of the first image. Curtis and I have filed a ticket to correct for
> this in the future, but is there a way to get the dimensions of an
> individual image in a tiff stack? (The first image in my stack is
> 1008x3008, and the last one is supposed to be like 40000x70000. I need
> the exact dimensions of the last image.)

For others' reference: https://github.com/scifio/scifio/issues/159

Ajeet: SCIFIO has a low-level TIFF API you can use to do it:
https://github.com/scifio/scifio/blob/master/scifio/src/main/java/io/scif/formats/tiff/TiffParser.java
https://github.com/scifio/scifio/blob/master/scifio/src/main/java/io/scif/formats/tiff/IFD.java

See in particular IFD#getImageWidth() and IFD#getImageHeight().

Better would be to fix the bug in SCIFIO's TiffFormat, such that it reports
a different Image per plane size. Want to try your hand at it? Mark and I
would be happy to answer any technical questions.

-Curtis


On Sun, May 11, 2014 at 12:58 PM, Johannes Schindelin
<schindelin at wisc.edu>wrote:

> Hi Ajeet,
>
> On Sun, 11 May 2014, Ajeet Vivekanandan wrote:
>
> > I finished the Ventana ROI to WiscScan converter (FIJI/ImageJ plugin).
> > There is only one issue that I would need Johannes's help for, but I'm
> > ready to test/use this as soon as that's done.
> >
> > Johannes, I have a tiff image stack of images all of different width and
> > height. When reading with the bioformats importer, it assumes that all
> > images are the same size and sets the width/height for all images to
> > that of the first image. Curtis and I have filed a ticket to correct for
> > this in the future, but is there a way to get the dimensions of an
> > individual image in a tiff stack? (The first image in my stack is
> > 1008x3008, and the last one is supposed to be like 40000x70000. I need
> > the exact dimensions of the last image.)
>
> If you are talking about an ImageJ 1.x style ImageStack data structure:
> this data structure can only contain images of identical X/Y dimension.
> There is simply no way to represent a collection of images with different
> dimensions as a single ImageStack.
>
> Ciao,
> Johannes
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://scif.io/pipermail/scifio/attachments/20140512/76552d68/attachment-0002.html>