search

abria / TeraStitcher

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

is voxel size option for Z step used at all? #37

Closed pawlowska closed 5 years ago

pawlowska commented 5 years ago

I am preparing batch script for stitching based on the one provided with the example dataset (the one with 7 rar files). We have datasets with different Z voxel sizes and we use image sequences and the XXXXXX_YYYYYY_ZZZZZZ file naming scheme where the correct Z is encoded. I noticed that with this naming scheme, the --vxl3 parameter doesn't seem to make any difference in either import or saving merged data. Is this correct?

iannellog commented 5 years ago

Monika, the vxl parameters affect only the naming of the output files (i.e. files generated by the -6/--merge step of TeraStitcher or by TeraConverter). In other words, if --vxl3=1.0, then the ZZZZZZ substring of the names is generated with step 10, i.e. 000000, 000010, 000020, etc. (the string encode the Z position in tenth of micron), if --vxl3=3.0, then names are generated with a step of 30, i.e. 000000, 000030, 000060, etc., and so on. The vxl parameters are also stored in the xml files and in the data.bin so they might be used by external tools to compute the physical position of a given voxel. If physical position of voxel does not matter for you, you can set vxl3 to any value. This will have effect on the names of the output files only. Best.

-- Giulio

Il giorno gio 11 ott 2018 alle ore 12:55 Monika Pawlowska < notifications@github.com> ha scritto:

I am preparing batch script for stitching based on the example provided with the example dataset (the one with 7 rar files). We have datasets with different Z voxel sizes and we use image sequences and the XXXXXX_YYYYYY_ZZZZZZ file naming scheme where the correct Z is encoded. I noticed that with this naming scheme, the --vxl3 parameter doesn't seem to make any difference in either import or saving merged data. Is this correct?

— 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/37, or mute the thread https://github.com/notifications/unsubscribe-auth/AIdv1sXzyf72EZuALpIiLTK0F64n2TNJks5ujyOMgaJpZM4XXSeM .

--

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

Ok, thanks!