Bug in output from Grid/Collection stitching plugin?

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Bug in output from Grid/Collection stitching plugin?

Straub, Volko A. (Dr.)
I have used the Grid/Collection stitching plugin to stitch a 5x6 mosaic of images. The approximate image position was defined by the metadata and was refined by the stitching plugin using the 'Compute overlap' option. The tiling was completed successfully and produced a reasonable image.
I now want to use the same tile coordinates and apply them to a second set of images. However, I have encountered two issues:

  1.  The image file names in the text file that is created and holds the image coordinates are all the same (the name of the first file in the sequence). Here is a copy of the first 6 lines that define the image coordinates. Note that the file name for all images is shown as 'MMStack_2-Pos000_000.ome.tif'

# Define the image coordinates
MMStack_2-Pos000_000.ome.tif; ; (0.0, 0.0)
MMStack_2-Pos000_000.ome.tif; ; (0.0, 0.0)
MMStack_2-Pos000_000.ome.tif; ; (0.0, 0.0)
MMStack_2-Pos000_000.ome.tif; ; (1339.3154121172638, -65.07994908143905)
MMStack_2-Pos000_000.ome.tif; ; (2626.3157710343603, -125.07998815471956)
MMStack_2-Pos000_000.ome.tif; ; (2672.3157710343603, 805.9200118452804)
...

  2.
If I manually rename the file names in the list and use this configuration file to stitch a second set of images ('Positions form file', 'Defined by TileConfiguration'), I end up with a stitch image of the correct dimensions, but where every tile is a copy of the first image in sequence.

I suspect that the problem is related to the fact that the first two tiles (0,0 and 1,0) only show a relative uniform background and are ignored in the final stitched image. In order to work around the issue, I can create sub-arrays of the overall image, tile those and then use the pairwise stitching, but it makes it all a bit more difficult/time consuming.
Does anybody have any thoughts/suggestions?

Thanks,
Volko


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Re: Bug in output from Grid/Collection stitching plugin?

MChapman
 I don't think I have seen any replies to this yet.
I have spent a lot of time working with the Grid collection/Stitching algorithm, but haven't specifically used "defined by metadata" at all.  First, I would recommend downloading the most recent version of Fiji as that fixed a ton of issues that I have been having recently.If that doesn't fix it, let me know as there are a few ways I know that a solution can be hacked together (all of it would be with scripts, essentially extracting the image names and locations manually from the metadata and fixing the TileConfiguration.txt file to allow the ReStitch)
Thanks!
Mike
    On Tuesday, April 14, 2020, 03:27:05 AM EDT, Straub, Volko A. (Dr.) <[hidden email]> wrote:  
 
 I have used the Grid/Collection stitching plugin to stitch a 5x6 mosaic of images. The approximate image position was defined by the metadata and was refined by the stitching plugin using the 'Compute overlap' option. The tiling was completed successfully and produced a reasonable image.
I now want to use the same tile coordinates and apply them to a second set of images. However, I have encountered two issues:

  1.  The image file names in the text file that is created and holds the image coordinates are all the same (the name of the first file in the sequence). Here is a copy of the first 6 lines that define the image coordinates. Note that the file name for all images is shown as 'MMStack_2-Pos000_000.ome.tif'

# Define the image coordinates
MMStack_2-Pos000_000.ome.tif; ; (0.0, 0.0)
MMStack_2-Pos000_000.ome.tif; ; (0.0, 0.0)
MMStack_2-Pos000_000.ome.tif; ; (0.0, 0.0)
MMStack_2-Pos000_000.ome.tif; ; (1339.3154121172638, -65.07994908143905)
MMStack_2-Pos000_000.ome.tif; ; (2626.3157710343603, -125.07998815471956)
MMStack_2-Pos000_000.ome.tif; ; (2672.3157710343603, 805.9200118452804)
...

  2.
If I manually rename the file names in the list and use this configuration file to stitch a second set of images ('Positions form file', 'Defined by TileConfiguration'), I end up with a stitch image of the correct dimensions, but where every tile is a copy of the first image in sequence.

I suspect that the problem is related to the fact that the first two tiles (0,0 and 1,0) only show a relative uniform background and are ignored in the final stitched image. In order to work around the issue, I can create sub-arrays of the overall image, tile those and then use the pairwise stitching, but it makes it all a bit more difficult/time consuming.
Does anybody have any thoughts/suggestions?

Thanks,
Volko


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Re: Bug in output from Grid/Collection stitching plugin?

Straub, Volko A. (Dr.)
Thanks Mike,
I had updated to Fiji/ImageJ v1.52v and applied all the latest plugin updates. I have now also tried updating to the latest nightly build, and the problems still persist, i.e. the generated tile configuration file shows the same file name for all positions. So, I assume that there is a bug in the code that leads to the filename in the tile configuration file not being updated properly.
Anyway, as this was pretty much a one off job, I spend a bit using a combination of pairwise stitching and manual alignment/arrangement to get the required output.
Cheers,
Volko


________________________________
From: mike chapman <[hidden email]>
Sent: 21 April 2020 20:05
To: [hidden email] <[hidden email]>
Subject: Re: Bug in output from Grid/Collection stitching plugin?

I don't think I have seen any replies to this yet.
I have spent a lot of time working with the Grid collection/Stitching algorithm, but haven't specifically used "defined by metadata" at all.  First, I would recommend downloading the most recent version of Fiji as that fixed a ton of issues that I have been having recently.If that doesn't fix it, let me know as there are a few ways I know that a solution can be hacked together (all of it would be with scripts, essentially extracting the image names and locations manually from the metadata and fixing the TileConfiguration.txt file to allow the ReStitch)
Thanks!
Mike
    On Tuesday, April 14, 2020, 03:27:05 AM EDT, Straub, Volko A. (Dr.) <[hidden email]> wrote:

 I have used the Grid/Collection stitching plugin to stitch a 5x6 mosaic of images. The approximate image position was defined by the metadata and was refined by the stitching plugin using the 'Compute overlap' option. The tiling was completed successfully and produced a reasonable image.
I now want to use the same tile coordinates and apply them to a second set of images. However, I have encountered two issues:

  1.  The image file names in the text file that is created and holds the image coordinates are all the same (the name of the first file in the sequence). Here is a copy of the first 6 lines that define the image coordinates. Note that the file name for all images is shown as 'MMStack_2-Pos000_000.ome.tif'

# Define the image coordinates
MMStack_2-Pos000_000.ome.tif; ; (0.0, 0.0)
MMStack_2-Pos000_000.ome.tif; ; (0.0, 0.0)
MMStack_2-Pos000_000.ome.tif; ; (0.0, 0.0)
MMStack_2-Pos000_000.ome.tif; ; (1339.3154121172638, -65.07994908143905)
MMStack_2-Pos000_000.ome.tif; ; (2626.3157710343603, -125.07998815471956)
MMStack_2-Pos000_000.ome.tif; ; (2672.3157710343603, 805.9200118452804)
...

  2.
If I manually rename the file names in the list and use this configuration file to stitch a second set of images ('Positions form file', 'Defined by TileConfiguration'), I end up with a stitch image of the correct dimensions, but where every tile is a copy of the first image in sequence.

I suspect that the problem is related to the fact that the first two tiles (0,0 and 1,0) only show a relative uniform background and are ignored in the final stitched image. In order to work around the issue, I can create sub-arrays of the overall image, tile those and then use the pairwise stitching, but it makes it all a bit more difficult/time consuming.
Does anybody have any thoughts/suggestions?

Thanks,
Volko


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