Merged data is not saved as a tiled image

[kirda]

Hi,

thank you for this great tool. It is a great help for large imaging datasets.

I noticed a problem. Only the low resolution outputs are saved as one tiled image. The others are saved in folders and subfolders containing separate images. This happens also if I select "bigtiff". Is there a special way to open/visualize this folder-system as a tile? Preferably, is there a way to get it saved as one tile in a single tiff?

Thank you, Daniel

[iannellog]

2017-09-05 10:00 GMT+02:00 kirda notifications@github.com:

Hi,

thank you for this great tool. It is a great help for large imaging datasets.

I noticed a problem. Only the low resolution outputs are saved as one tiled image. The others are saved in folders and subfolders containing separate images. This happens also if I select "bigtiff".

in the Merge panel (I suppose you are using the GUI version of the tool) when you choose "TIFF (tiled, 3D)" as an output format (again I suppose this is your case), at the right, three edit cells appear specifying the approximate size of the tiles to be generated. If you want to generate just a single multipage tiff you have to put in these cells a number larger than the final size of the stitched image (reported above for each resolution). I apologize if this is not very user-friendly :-)

Is there a special way to open/visualize this folder-system as a tile? Preferably, is there a way to get it saved as one tile in a single tiff?

see the answer above. Consider however the final size of your image: most visualization tools crash or hang if the file is too big. If you have or plan to have very big files (hundreds of GB or more) some form of tiling would be needed to make the images tractable. Let me know if this could be a problem for you because I might have some useful suggestions.

Best.

-- Giulio

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Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy

Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google.it/citations?user=L-UJxIgAAAAJ

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[kirda]

Dear Giulio,

thank you for the rapid response. I thought about something like this, but the problem is that I cannot set those values higher than 999.

Is there a way around?

Thank you, Daniel

[iannellog]

You are right, I never realized this problem, because I generally use the command line version for large images.

We will fix the problem, but in the mean time you can proceed as follows.

Check if you have downloaded the executable of the tool named "teraconverter" Instead of using the Merge panel of the GUI, launch a command like:

./teraconverter --sfmt="TIFF (unstitched, 3D)" -s=SSS --dfmt="TIFF (tiled, 3D)" -d=DDD

where: SSS is the complete path of the xml_merging.xml file generated by the GUI after the Align step DDD is the path of the directory where you want to generate the stitched image

If you want to generate more resolutions or resolutions different from the highest one add the option:

--resolutions=XXX

where XXX is a string of digits (0 means the highest resolution, 1 the next one, etc.) for instance the option:

--resolutions=024

generates the highest, skips the next, generates the next, skips another, generates the next.

For more details, besides launching the command

./teraconverter -h,

at link https://github.com/abria/TeraStitcher/wiki, on the right panel, you can download the "TeraTools guide", which is intended for advanced user and documents most (not all) features of our tools. If you have questions, please write me again.

Best.

-- Giulio

2017-09-05 11:44 GMT+02:00 kirda notifications@github.com:

Dear Giulio,

thank you for the rapid response. I thought about something like this, but the problem is that I cannot set those values higher than 999.

Is there a way around?

Thank you, Daniel

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/abria/TeraStitcher/issues/20#issuecomment-327126372, or mute the thread https://github.com/notifications/unsubscribe-auth/AIdv1vLIjUi9nfz2G_8FVZsRa2Ti90MHks5sfRf2gaJpZM4PMkzX .

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Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy

Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google.it/citations?user=L-UJxIgAAAAJ

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[abria]

We have fixed the bug. The output format option "TIFF 3D" was previously disabled since we needed further testing with big tiffs. Now you can select it. You don't need to set any dimensions in this case.

Please try the new TeraStitcher version 1.10.6 at this link and let us know if it works so we can make a new release.

Please note that if the image is too big (> 2 GB), you can still experience some issues when saving the image. In this case you will need to select the big tiff option.

Thanks.

[kirda]

Dear all,

thanks for being so helpful. I got it to work with the cmd line version. (The stitched image is 83 Gb, Fiji is handling it as virtual stack)

I will try the second part of the dataset with the new GUI version. However, I need some time to re-save my data in Fiji as image sequence, as it didn't work for me with 3d Tiff as an input. I had to do this reformatting step for the dataset which I stitched now too.

I will let you know.

best daniel