Re: stitching troubleshoot

Posted by chanjeh on Jun 27, 2013; 8:07am
URL: http://imagej.273.s1.nabble.com/stitching-troubleshoot-tp4999134p5003675.html

Hi,
I'm sorry I can't help you directly.
I also post a question still unsolved,
but it is maybe related to your problem.

Well, I take timelapse, multiposition XY images (micromanager, very simple).
My images are almost black, waiting for some fluorescence (but I don't know where it will come).

As expected, automated Grid/Collection Stitching is not working at all.
My strategie is to take a first XY serie of images (a single time point) with brightfield.
This way, I can obtain a tileconfiguration.txt file with XY images real coordinates.

Being confident in the reproducibility of my XY stage movement, I would like then to make the stitching using Grid/Collection Stitching > Position from file; Defined by TileConfiguration (without compute overlap, ie 'manual' alignment)

with a file looking like this, create by myself (to add an artificial Z):

# Define the number of dimensions we are working on
dim = 3

# Define the image coordinates
img_000.tif; ; (0.0, 0.0, 0.0)
img_001.tif; ; (466.7324, -5.0000305, 0.0)
img_002.tif; ; (933.46655, -10.000092, 0.0)
img_003.tif; ; (5.2659836, 465.99997, 0.0)
img_004.tif; ; (472.46664, 460.99994, 0.0)
img_005.tif; ; (938.46655, 455.9999, 0.0)
img_006.tif; ; (10.332681, 931.99994, 0.0)
img_007.tif; ; (477.3997, 926.99994, 0.0)
img_008.tif; ; (943.46655, 921.9999, 0.0)

# Define the image coordinates
img_009.tif; ; (0.0, 0.0, 50.0)
img_010.tif; ; (466.7324, -5.0000305, 50.0)
img_011.tif; ; (933.46655, -10.000092, 50.0)
img_012.tif; ; (5.2659836, 465.99997, 50.0)
img_013.tif; ; (472.46664, 460.99994, 50.0)
img_014.tif; ; (938.46655, 455.9999, 50.0)
img_015.tif; ; (10.332681, 931.99994, 50.0)
img_016.tif; ; (477.3997, 926.99994, 50.0)
img_017.tif; ; (943.46655, 921.9999, 50.0)

...

Unfortunately, I never succeeded, and have to proceed in 2D, YX layer by XY layer... which works well but is time consuming.

Maybe it is a solution for you: work with tileconfiguration.
But as already said, dim=3 doesn't work for me... if you have an idea from your side?

Sincerely,
Chan