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abria / TeraStitcher

A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images
http://abria.github.io/TeraStitcher/
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Saving merged images in a single file larger than 4GB #14

Open pawlowska opened 7 years ago

pawlowska commented 7 years ago

Is it possible to save the stitched image in a single file (rather than image series) if it's larger than 4GB? The website states "New version 1.9.63 adds support for Big TIFF (tif files larger than 2 GB)" but when I tried to save a big merged file, only the first 42 slices corresponding to 4GB of data were saved, even though the GUI claimed that it was merging all the slices and didn't show any error message. Using version 1.9.67

abria commented 7 years ago

Could you please post a screenshot of the settings in the "Merge" step? Thanks

pawlowska commented 7 years ago

I restarted the GUI. I think it was: 3Dseries, tiff3D, tif (the default), 16bits, all channels, but I can try to reproduce again later.

abria commented 7 years ago

How were the height, width, and depth spinboxes set?

pawlowska commented 7 years ago

height and width were not available in this setting , depth was set to the full number of slices shown under "Resolution" in the choice of Outputs, which for this particular case was 458.

iannellog commented 7 years ago

We included an implementation of BigTiff in out tools. I tested that it can read BigTiff files, but I do not remember if I tried to generate images larger than 4 GB (probably not). I will do some test and then I will write you again.

-- Giulio

2017-03-28 13:13 GMT+02:00 Monika Pawlowska notifications@github.com:

Is it possible to save the stitched image in a single file (rather than image series) if it's larger than 4GB? The website states "New version 1.9.63 adds support for Big TIFF (tif files larger than 2 GB)" but when I tried to save a big merged file, only the first 42 slices corresponding to 4GB of data were saved, even though the GUI claimed that it was merging all the slices and didn't show any error message. Using version 1.9.67

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/abria/TeraStitcher/issues/14, or mute the thread https://github.com/notifications/unsubscribe-auth/AIdv1rgVUmRVE-PJ7I_fK4nUlyV-u_1hks5rqOtxgaJpZM4MreLQ .

--

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

iannellog commented 7 years ago

Although there is a few information about BigTiff, I understand (but I have still to check) that you have to specify that a file must be BigTiff when it is created. If a file is not created as a BigTiff and during generation it overcomes 4GB, the library raises an error (see for instance this page http://www.gdal.org/frmt_gtiff.html searching for "Control whether the created file is a BigTIFF or a classic TIFF"). Currently our interface to libtiff does not support the creation of BigTiff files. I can easily add this feature in the next release (of course after some testing). I only need still a few days because I am doing several improvements to the code and I cannot release a new version until I finish. I will inform you when BigTiff is fully suppported. Best.

-- Giulio

2017-03-28 13:13 GMT+02:00 Monika Pawlowska notifications@github.com:

Is it possible to save the stitched image in a single file (rather than image series) if it's larger than 4GB? The website states "New version 1.9.63 adds support for Big TIFF (tif files larger than 2 GB)" but when I tried to save a big merged file, only the first 42 slices corresponding to 4GB of data were saved, even though the GUI claimed that it was merging all the slices and didn't show any error message. Using version 1.9.67

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/abria/TeraStitcher/issues/14, or mute the thread https://github.com/notifications/unsubscribe-auth/AIdv1rgVUmRVE-PJ7I_fK4nUlyV-u_1hks5rqOtxgaJpZM4MreLQ .

--

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

pawlowska commented 7 years ago

It's not urgent - I just wanted to make sure if it's not supported or I'm doing something wrong.

iannellog commented 7 years ago

Monika, we have released a version of the tools that can generate BigTiff files. To do that you have to use TeraConverter in place of the last step of TeraStitcher, specifying one of the following output formats (option --dfmt):

"TIFF (series, 2D)" "TIFF (tiled, 2D)" "TIFF (tiled, 3D)" "TIFF (tied, 4D)"

if the size of a file generated is larger than 4GB, it is automatically generated using the BigTiff format independently of the file is compressed or not. If you want to generate a BigTiff file independently of its size you must specify the option --libtiff_bigtiff in the command line.

General information about TeraConverter can be found in the supplementary material of the paper:

Bria A, Iannello G, Onofri L, Peng H , “TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images”, Nature Methods, February 25, 2016

Other information on TeraConverter/Paraconverter can be found on our site ( https://github.com/abria/TeraStitcher/wiki). For using TeraConverter in place of the last step of TeraStitcher have a look to the attached file.

Best.

-- Giulio

2017-03-29 12:04 GMT+02:00 Monika Pawlowska notifications@github.com:

It's not urgent - I just wanted to make sure if it's not supported or I'm doing something wrong.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/abria/TeraStitcher/issues/14#issuecomment-290044130, or mute the thread https://github.com/notifications/unsubscribe-auth/AIdv1v2AQXiQ0GNwfGkIXrGqSpmcH7Dfks5rqiy_gaJpZM4MreLQ .

--

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