stitching troubleshoot

[Suleiman]

Hi ImageJ users,

I am having some trouble stitching time lapse videos using the pairwise and 3d pluggins. Some of the images stitch, some of them don't and am not sure why that is the case.

My initial images were acquired on a spinning disc microscope using volocity. I have different Z stacks  taken of up to 30 different (XY) regions over a 6-10h period. I am exporting the individual stacks from volocity as tiffs and importing to imageJ as hyperstacks. I take Z projections and  then attempt to stitch them using the Pairwise Stitching/3D pluggins. I would like to see the stacks stitched so that neighbouring XY regions are next to each other, with some overlap. However, this does not always happen. Some stacks stitch with some overlap, others overlap completely and look like 1 stack, and others do not stitch at all.

all stacks have the same XYZT parameters,they are all 8 bit. Original video saved as .mvd2 on volocity, in the raw data files all are .atsf  

Any advice/tips would be appreciated

Thanks,
Suleiman

[chanjeh]

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