http://imagej.273.s1.nabble.com/TrakEM2-Stitching-overlapping-images-from-coordinates-tp5011918p5011930.html
> Hi Peter,
>
> yes. This is an intrinsic limitation of ImageJ's and AWT's internal
> data structure which stores 2d image planes in integer indexed arrays.
> I.e. 2d images cannot be larger than 2GPixel (e.g. 45k x 45k). TrakEM2
> and ImgLib2 enable to generate and visualize larger images but you
> cannot generate a single image export for use in ImageJ or AWT (see
> above). Instead, you can export tiles and use a tile based viewer or
> other external tools to combine them into a single image.
>
> Best,
> Stephan
>
>
>
> On Mon, 2015-03-09 at 13:24 +0100, Peter Haub wrote:
>> Hi Andre
>> and everybody who may concerned,
>>
>> we are also facing a memory problem stitching 4000 images using the
>> Grid/Collection stitching plugin.
>> Our 8bit image has a size of more then 12 GByte (or > 12 GPixel).
>>
>> I wonder if this could have something to do with the integer type
>> definition of the 'index' variable in the ByteArray.setValue function:
>> public void setValue( final int index, final byte value )
>>
>>
>> The error message is:
>>
>> (Fiji Is Just) ImageJ 2.0.0-rc-23/1.49m; Java 1.6.0_24 [64-bit]; Windows
>> 7 6.1; 16857MB of 20000MB (84%)
>>
>> java.lang.ArrayIndexOutOfBoundsException: -1741201634
>>
>> at
>> net.imglib2.img.basictypeaccess.array.ByteArray.setValue(ByteArray.java:68)
>>
>> at
>> net.imglib2.type.numeric.integer.GenericByteType.setValue(GenericByteType.java:101)
>>
>> at
>> net.imglib2.type.numeric.integer.UnsignedByteType.set(UnsignedByteType.java:161)
>>
>> at
>> net.imglib2.type.numeric.integer.UnsignedByteType.setInteger(UnsignedByteType.java:179)
>>
>> at
>> net.imglib2.type.numeric.integer.AbstractIntegerType.setReal(AbstractIntegerType.java:67)
>>
>> at mpicbg.stitching.fusion.Fusion.writeTile(Fusion.java:1017)
>>
>> at mpicbg.stitching.fusion.Fusion.writeTile(Fusion.java:972)
>>
>> at mpicbg.stitching.fusion.Fusion.writeTile(Fusion.java:977)
>>
>> at mpicbg.stitching.fusion.Fusion.writeBlock(Fusion.java:916)
>>
>> at mpicbg.stitching.fusion.Fusion.fuse(Fusion.java:224)
>>
>> at plugin.Stitching_Grid.run(Stitching_Grid.java:590)
>>
>>
>> Regards,
>> Peter
>>
>>
>>
>> On 09.03.2015 04:26, Andre Pereira wrote:
>>> Hi everybody,
>>>
>>> We are trying to stitch a very large dataset (~90GB) of overlapping images. We used the Grid/collection stitching plugin, which was able to stitch the images correctly in smaller datasets, but we ran into memory problems with the larger ones. We then switched to TrakEM2 which is doing a great job at handling the large ones.
>>>
>>> We are, however, facing a problem with the positioning of the tiles. After importing the images using a text file with the coordinates, the tiles are not positioned in the exact position. There is a small, but important shift. We verified our coordinates in the text file and they are correct. Our reconstructions with the Grid/collection stitching plugin, for instance, are accurate.
>>>
>>> Has anyone had this problem before?
>>>
>>> Thanks for your help!
>>>
>>> Kind regards,
>>> Andre Pereira
>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>
>>>
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