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Image Stitching problem

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Jirka
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Image Stitching problem

Jirka
This post was updated on .
Good morning
I have com difficulty with the ImageJ Stitching Plugins. I used it some
time ago without any problem, I made a macro for several image series,
which now does not work. Well I need to merge together row of 9 images so I
used following command (I used the same images and the same configuration
as I had used 2 years ago and it worked fine):

run("Grid/Collection stitching", "type=[Grid: snake by rows] order=[Right &
Down                ] grid_size_x=9 grid_size_y=1 tile_overlap=5
first_file_index_i=0
directory=/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif
file_names=29-041-Izd2-Cc10-5-les1_p{ii}.tif
output_textfile_name=TileConfiguration-test.txt fusion_method=[Linear
Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50
absolute_displacement_threshold=3.50 subpixel_accuracy
computation_parameters=[Save memory (but be slower)] image_output=[Fuse and
display]");

But in the end it pastes 9 times the first image in row by size of 9
consecutive frames and the log is following:

Stitching internal version: 1.1
Loading (0, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p00.tif
...
2080x1540px, channels=3, timepoints=1 (899 ms)
Loading (1, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p01.tif
...
2080x1540px, channels=3, timepoints=1 (893 ms)
Loading (2, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p02.tif
...
2080x1540px, channels=3, timepoints=1 (905 ms)
Loading (3, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p03.tif
...
2080x1540px, channels=3, timepoints=1 (876 ms)
Loading (4, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p04.tif
...
2080x1540px, channels=3, timepoints=1 (903 ms)
Loading (5, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p05.tif
...
2080x1540px, channels=3, timepoints=1 (863 ms)
Loading (6, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p06.tif
...
2080x1540px, channels=3, timepoints=1 (890 ms)
Loading (7, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p07.tif
...
2080x1540px, channels=3, timepoints=1 (894 ms)
Loading (8, 0):
/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p08.tif
...
2080x1540px, channels=3, timepoints=1 (876 ms)
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
0.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
1976.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
3952.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
5928.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
7904.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
9880.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
11856.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
13832.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
15808.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
Fuse & Display ...
Finished fusion (4777 ms)
Finished ... (12785 ms)

It seems to find fine transformation but I think that the problem is that
it pastes always Tile #1. What am I doing wrong or is there a bug?

Thanks
--
Best regards, Jiri Borovec
----------------------------------------------------------------------------------------------------
Jiří Borovec <jiri.borovec@fel.cvut.cz>
PhD student at CMP CTU, ISC member
http://cmp.felk.cvut.cz/~borovji3

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Stephan Preibisch
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Re: Image Stitching problem

Stephan Preibisch
Hi Jiri,

it seems it does not compute anything and just loads the images and puts them all on top of each other. Can you try doing the same thing without the macro, i.e. doing it by hand?

Cheers,
Stephan
---

Dr. Stephan Preibisch
HFSP Fellow
Robert H. Singer / Eugene Myers lab

Albert Einstein College of Medicine / HHMI Janelia Farm / MPI-CBG

email: [hidden email] / [hidden email] / [hidden email]
web: http://www.preibisch.net/


On Jun 27, 2014, at 13:04 , Jiří Borovec <[hidden email]> wrote:

> Good morning
> I have com difficulty with the ImageJ Stitching Plugins. I used it some
> time ago without any problem, I made a macro for several image series,
> which now does not work. Well I need to merge together row of 9 images so I
> used following command (I used the same images and the same configuration
> as I had used 2 years ago and it worked fine):
>
> run("Grid/Collection stitching", "type=[Grid: snake by rows] order=[Right &
> Down                ] grid_size_x=9 grid_size_y=1 tile_overlap=5
> first_file_index_i=0
> directory=/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif
> file_names=29-041-Izd2-Cc10-5-les1_p{ii}.tif
> output_textfile_name=TileConfiguration-test.txt fusion_method=[Linear
> Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50
> absolute_displacement_threshold=3.50 subpixel_accuracy
> computation_parameters=[Save memory (but be slower)] image_output=[Fuse and
> display]");
>
> But in the end it pastes 9 times the first image in row by size of 9
> consecutive frames and the log is following:
>
> Stitching internal version: 1.1
> Loading (0, 0):
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p00.tif
> ...
> 2080x1540px, channels=3, timepoints=1 (899 ms)
> Loading (1, 0):
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p01.tif
> ...
> 2080x1540px, channels=3, timepoints=1 (893 ms)
> Loading (2, 0):
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p02.tif
> ...
> 2080x1540px, channels=3, timepoints=1 (905 ms)
> Loading (3, 0):
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p03.tif
> ...
> 2080x1540px, channels=3, timepoints=1 (876 ms)
> Loading (4, 0):
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p04.tif
> ...
> 2080x1540px, channels=3, timepoints=1 (903 ms)
> Loading (5, 0):
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p05.tif
> ...
> 2080x1540px, channels=3, timepoints=1 (863 ms)
> Loading (6, 0):
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p06.tif
> ...
> 2080x1540px, channels=3, timepoints=1 (890 ms)
> Loading (7, 0):
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p07.tif
> ...
> 2080x1540px, channels=3, timepoints=1 (894 ms)
> Loading (8, 0):
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p08.tif
> ...
> 2080x1540px, channels=3, timepoints=1 (876 ms)
> 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> 0.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> 1976.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> 3952.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> 5928.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> 7904.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> 9880.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> 11856.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> 13832.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> 15808.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> Fuse & Display ...
> Finished fusion (4777 ms)
> Finished ... (12785 ms)
>
> It seems to find fine transformation but I think that the problem is that
> it pastes always Tile #1. What am I doing wrong or is there a bug?
>
> Thanks
> --
> Best regards, Jiri Borovec
> ----------------------------------------------------------------------------------------------------
> Ing. Jiri Borovec, MSc                           <[hidden email]>
> PhD student at CMP CTU, member ISC  |       tel.: +420 2 2435 7590
> http://cmp.felk.cvut.cz/~borovji3             |    mob.: +420 728 480 285
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Jirka
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Re: Image Stitching problem

Jirka
This post was updated on .
Hello Stephan,
I tried the Stitching by hand and just used the macro recording (and paste
the recorded macro) to "illustrate" consequence of used steps and
parameters.

Jirka
--
Best regards, Jiri Borovec
----------------------------------------------------------------------------------------------------
Jiří Borovec <jiri.borovec@fel.cvut.cz>
PhD student at CMP CTU, ISC member
http://cmp.felk.cvut.cz/~borovji3


On 28 June 2014 00:21, Stephan Preibisch <preibisch@mpi-cbg.de> wrote:

> Hi Jiri,
>
> it seems it does not compute anything and just loads the images and puts
> them all on top of each other. Can you try doing the same thing without the
> macro, i.e. doing it by hand?
>
> Cheers,
> Stephan
> ---
>
> Dr. Stephan Preibisch
> HFSP Fellow
> Robert H. Singer / Eugene Myers lab
>
> Albert Einstein College of Medicine / HHMI Janelia Farm / MPI-CBG
>
> email: stephan.preibisch@einstein.yu.edu / preibischs@janelia.hhmi.org /
> preibisch@mpi-cbg.de
> web: http://www.preibisch.net/
>
>
> On Jun 27, 2014, at 13:04 , Jiří Borovec <jiri.borovec@fel.cvut.cz> wrote:
>
> > Good morning
> > I have com difficulty with the ImageJ Stitching Plugins. I used it some
> > time ago without any problem, I made a macro for several image series,
> > which now does not work. Well I need to merge together row of 9 images
> so I
> > used following command (I used the same images and the same configuration
> > as I had used 2 years ago and it worked fine):
> >
> > run("Grid/Collection stitching", "type=[Grid: snake by rows]
> order=[Right &
> > Down                ] grid_size_x=9 grid_size_y=1 tile_overlap=5
> > first_file_index_i=0
> >
> directory=/home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif
> > file_names=29-041-Izd2-Cc10-5-les1_p{ii}.tif
> > output_textfile_name=TileConfiguration-test.txt fusion_method=[Linear
> > Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50
> > absolute_displacement_threshold=3.50 subpixel_accuracy
> > computation_parameters=[Save memory (but be slower)] image_output=[Fuse
> and
> > display]");
> >
> > But in the end it pastes 9 times the first image in row by size of 9
> > consecutive frames and the log is following:
> >
> > Stitching internal version: 1.1
> > Loading (0, 0):
> >
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p00.tif
> > ...
> > 2080x1540px, channels=3, timepoints=1 (899 ms)
> > Loading (1, 0):
> >
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p01.tif
> > ...
> > 2080x1540px, channels=3, timepoints=1 (893 ms)
> > Loading (2, 0):
> >
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p02.tif
> > ...
> > 2080x1540px, channels=3, timepoints=1 (905 ms)
> > Loading (3, 0):
> >
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p03.tif
> > ...
> > 2080x1540px, channels=3, timepoints=1 (876 ms)
> > Loading (4, 0):
> >
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p04.tif
> > ...
> > 2080x1540px, channels=3, timepoints=1 (903 ms)
> > Loading (5, 0):
> >
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p05.tif
> > ...
> > 2080x1540px, channels=3, timepoints=1 (863 ms)
> > Loading (6, 0):
> >
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p06.tif
> > ...
> > 2080x1540px, channels=3, timepoints=1 (890 ms)
> > Loading (7, 0):
> >
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p07.tif
> > ...
> > 2080x1540px, channels=3, timepoints=1 (894 ms)
> > Loading (8, 0):
> >
> /home.dokt/borovji3/datagrid/microscopy/CIMA/images-lesions_original/frames/29-041-Izd2-w35-Cc10-5-les1_tif/29-041-Izd2-Cc10-5-les1_p08.tif
> > ...
> > 2080x1540px, channels=3, timepoints=1 (876 ms)
> > 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> > 0.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> > 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> > 1976.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> > 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> > 3952.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> > 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> > 5928.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> > 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> > 7904.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> > 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> > 9880.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> > 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> > 11856.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> > 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> > 13832.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> > 29-041-Izd2-Cc10-5-les1.tif - Tile #1: [3,3](AffineTransform[[1.0, 0.0,
> > 15808.0], [0.0, 1.0, 0.0]]) 1.7976931348623157E308
> > Fuse & Display ...
> > Finished fusion (4777 ms)
> > Finished ... (12785 ms)
> >
> > It seems to find fine transformation but I think that the problem is that
> > it pastes always Tile #1. What am I doing wrong or is there a bug?
> >
> > Thanks
> > --
> > Best regards, Jiri Borovec
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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