Nice work! It seems like you have spent some time on this. Do you have
some code and/or images that can be useful for us? The image and data we
have access to are from Genepix 4.1.
I think that adding parameters for which image to use in a multi-image
TIFF should be easy to implement. This can be done earliest at the 2.4
release.
/Nicklas
Chad Matsalla wrote:
> Greetings!
>
> I've been troubleshooting a problem that exists when trying to use images
> generated by Genepix 6.0/6.1 as images for spots.
>
> Genepix generates a single, multi-image, 16 bit greyscale TIFF. It's
> composition is as follows:
> Index Description
> 1 635 preview (495x1396 pixels)
> 2 532 preview (495x1396 pixels)
> 3 635 image (1884x5472 pixels)
> 4 523 image (1884x5472)
>
> The image offsets and scales are found in the .gpr file that Genepix
> creates. I used those numbers to try to use the single-image tiff for spots
> but most of the time it failed with an exception that I described in
> previous posts:
> java.lang.ClassCastException: [[B
> at
> com.sun.media.jai.opimage.BandMergeOpImage.shortLoop(BandMergeOpImage.java:3
> 41)
>
> Once in a while, though, it would succeed but the spots would be tiny in the
> images.
>
> This is because BASE2 is using indices 1 and 2 for the images in a
> multi-image tiff. In the case of GenePix 6.0/6.1 these are preview images.
>
> If you select 'Export Images' in Genepix 6.0/6.1 it does not do what you
> expect. I would expect that it would run it's own version of tiffsplit and
> generate two 16-bit greyscale tiffs.
>
> It actually creates two RGB images with 8 bits in the appropriate colour
> channel - red or green. These images cannot be imported into BASE (they
> provide the same exception as above).
>
> The reason why this exception is so mysterious can be balmed on JAI. IN
> core/net/sf/basedb/core/SpotImages.java the method
> In private RenderedOp loadTiffImage(File file, int band)
> executes this:
> RenderedOp image = JAI.create("tiff", params);
> For the single-image tiffs described above, this call returns the equivalent
> of an empty image:
> (PlanarImage[minX=0 minY=0 width=0 height=0 tileGridXOffset=0
> tileGridYOffset=0 tileWidth=0 tileHeight=0 sampleModel=null
> colorModel=null])
>
> It's my opinion that this should somehow throw an exception either through
> JAI or have this condition be trapped by BASE because, well, the call
> CLEARLY failed.
>
> Can a developer have this throw an exception? It would make image parsing
> problems MUCH easier to find.
>
> RIGHT! Let's return to the problem of the images.
>
> As a user of Genepix, I cannot change it's exporting behavior. However,
> when I use 'tiffsplit' on the commandline to split the GenePix multi-image
> tiff and import each image (full-size, not preview) into BASE2 separately
> everything works. This implies that there is not a fundamental problem with
> the individual GenePix images (as found in the multi-image tiff).
>
> BASE1 had a feature in 'Create Spot Images' that allowed you to specify:
> 'Index of ch1 TIFF'
> 'Index of ch2 TIFF'
>
> Can you please bring back this feature in BASE2? In the meantime I will
> modify our local copy to do this without prompting.
>
> Thanks for your efforts!
>
> Chad Matsalla
> Plant Biotechnology Institute, National Research Council of Canada
> Saskatoon, Saskatchewan, Canada
>
>
>
>
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