search

abria / TeraStitcher

A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images
http://abria.github.io/TeraStitcher/
Other
78 stars 32 forks source link

wrongly stitched data although marked as 'stitchable' in xml #40

Open pawlowska opened 5 years ago

pawlowska commented 5 years ago

I have probably stitched hundreds of datasets in terastitcher already and most of it goes fine. However, sometimes there are errors in stitched data, even though in the xml all stacks are listed as STITCHABLE="yes". How do I proceed with debugging in such cases?

The example below was originally from a 3x4x559 dataset. I stitched a 2x2x559 subset again and the same error (ie incorrect shift that is visible with a naked eye after zooming in) is visible.

example_stitched_slice

iannellog commented 5 years ago

As I wrote you I have an alternative global positioning algorithm that performs better than the standard one. I will send you instruction about how to use it. In the mean time, could you please send me alla the xml files that TeraStitcher generates on your dataset (from xml_import.xml to aml_merging.xml)? Another useful information for me is if you use the GUI version or the command line one. Finally do you use a windows or linux platform? Best.

-- Giulio

Il giorno gio 25 ott 2018 alle ore 12:31 Monika Pawlowska < notifications@github.com> ha scritto:

I have probably astitched hundreds of datasets in terastitcher already and most of it goes fine. However, sometimes there are errors in stitched data, even though in the xml all stacks are listed as 'STITCHABLE="yes"'. How do I proceed with debugging in such cases?

The example below was originally from a 3x4x559 dataset. I stitched a 2x2x559 subset again and the same error (ie incorrect shift that is visible with a naked eye after zooming in) is visible.

[image: example_stitched_slice] https://user-images.githubusercontent.com/11158300/47494175-584a1200-d851-11e8-8cd3-e685da9d93ff.PNG

— 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/40, or mute the thread https://github.com/notifications/unsubscribe-auth/AIdv1ne08GpNPQiHAsQRfTSBcr1yCnhpks5uoZMJgaJpZM4X5-gc .

--

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 5 years ago

dear @iannellog did you receive my email?

In the meantime, I played with parameters and the one that improves the result somewhat is threshold. Originally it was 0.7. With 0.75 I have a better, although not perfect result.

iannellog commented 5 years ago

Il giorno mer 7 nov 2018 alle ore 09:15 Monika Pawlowska < notifications@github.com> ha scritto:

dear @iannellog https://github.com/iannellog did you receive my email?

which mail? I do not think I received mails from you recently

In the meantime, I played with parameters and the one that improves the result somewhat is threshold. Originally it was 0.7. With 0.75 I have a better, although not perfect result.

I have sent to you in a separate mail the instructions to test an alternative tile placement algorithm.

Best.

-- Giulio

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