http://imagej.273.s1.nabble.com/Image-Stitching-problem-tp5008473p5008479.html
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?
Dr. Stephan Preibisch
Robert H. Singer / Eugene Myers lab
> 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
>
> --
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