Re: TrakEM2: Stitching overlapping images from coordinates

Posted by ctrueden on Mar 09, 2015; 6:40pm
URL: http://imagej.273.s1.nabble.com/TrakEM2-Stitching-overlapping-images-from-coordinates-tp5011918p5011927.html

Hi Peter,

> 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).

ImageJ1 has a hard limit of 2 GPix per image plane. Since you are stitching
so many planes into a single fused image, you may be exceeding that limit.

It is a goal of ImageJ2 to overcome this limit, but there is still a long
road ahead.

In the meantime, you can stitch huge mosaics a piece at a time, or try
TrakEM2 -- though personally I am not able to help with TrakEM2 issues.

Regards,
Curtis


On Mon, Mar 9, 2015 at 7:24 AM, Peter Haub <[hidden email]> 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
>>
>>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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