Posted by
Rossi, Sharyn (NIH/NIA/IRP) [C] on
URL: http://imagej.273.s1.nabble.com/Grid-Stitching-no-output-image-tp5018380p5018468.html
Hi Stephan,
Thanks for your reply. It can wait until May – I will keep an eye out for BigStitcher.
Cheers,
Sharyn
On 4/7/17, 12:41 AM, "
[hidden email]" <
[hidden email]> wrote:
Hi, no, the channels will not help. Downsampling should, but the final fused image will most likely not be displayable either at full resolution. We are actually implementing a new version of the Stitching (the BigStitcher) that will be released in May. This will address exactly those problems. How urgent is your reconstruction, we could give you a preliminary version that already works to some extent (still requires to replace some jars manually in Fiji).
All the best,
Stephan
---
Dr. Stephan Preibisch
Group Leader
Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC)
Building 89, 1.08b
email:
[hidden email]<mailto:
[hidden email]>
web:
http://preibischlab.mdc-berlin.de
On 6 Apr 2017, at 16:55, Rossi, Sharyn (NIH/NIA/IRP) [C] <
[hidden email]<mailto:
[hidden email]>> wrote:
Hi Stephan,
Thanks for your reply. Yes – there are many images that were obtained using a light-sheet ultramicroscope so there is that in addition to the size of each individual image. I did select down sampling and cut the pixel size in half and I did specify the 20% overlap (although I also tried it without and obtained the same result). Do you think I should down-sample even more? I have 2 filters in the dataset so if you think it would help, I could separate the filters – stitch one color at a time and then overlay.
Thanks for your help,
Sharyn
On 4/6/17, 1:28 AM, "
[hidden email]<mailto:
[hidden email]>" <
[hidden email]<mailto:
[hidden email]>> wrote:
Hi, your images are too big for the current version (?>2^31 pixels) … which parameters do you use to run the Stitching? It seems to me you might not specify an approximate overlap between tiles?
Cheers,
Stephan
---
Dr. Stephan Preibisch
Group Leader
Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC)
Building 89, 1.08b
email:
[hidden email]<mailto:
[hidden email]><mailto:
[hidden email]>
web:
http://preibischlab.mdc-berlin.de
On 5 Apr 2017, at 21:26, Rossi, Sharyn (NIH/NIA/IRP) [C] <
[hidden email]<mailto:
[hidden email]><mailto:
[hidden email]>> wrote:
Hi,
Figured I would try this once again to see if anyone else has encountered a problem like this. I am attaching the log and console info.
Thanks,
Sharyn
On 3/27/17, 10:43 AM, "Rossi, Sharyn (NIH/NIA/IRP) [C]" <
[hidden email]<mailto:
[hidden email]><mailto:
[hidden email]>> wrote:
Hello,
I have run a large dataset obtained from an ultra-microscope through the grid-stitch plugin and although it generates an output.txt file and processes each of the images in the mosaic (as seen via console), I get no output image. I have tried writing to disk as well as the live stitch option to no avail. Any comments or suggestions as to what may be the problem?
Thanks,
Sharyn
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