NDLI: Three-dimensional alignment and merging of confocal microscopy stacks

Content Provider	IEEE Xplore Digital Library
Author	Ramesh, N. Otsuna, H. Tasdizen, T.
Copyright Year	2013
Description	Author affiliation: Dept. of Electr. & Comput. Eng., Univ. of Utah, Salt Lake City, UT, USA (Ramesh, N.; Tasdizen, T.) \|\| Dept. of Neurobiol. & Anatomy, Univ. of Utah, Salt Lake City, UT, USA (Otsuna, H.)
Abstract	We describe an efficient, robust, automated method for image alignment and merging of translated, rotated and flipped con-focal microscopy stacks. The samples are captured in both directions (top and bottom) to increase the SNR of the individual slices. We identify the overlapping region of the two stacks by using a variable depth Maximum Intensity Projection (MIP) in the z dimension. For each depth tested, the MIP images gives an estimate of the angle of rotation between the stacks and the shifts in the x and y directions using the Fourier Shift property in 2D. We use the estimated rotation angle, shifts in the x and y direction and align the images in the z direction. A linear blending technique based on a sigmoidal function is used to maximize the information from the stacks and combine them. We get maximum information gain as we combine stacks obtained from both directions.
Starting Page	1447
Ending Page	1450
File Size	4408189
Page Count	4
File Format	PDF
ISBN	9781479923410
DOI	10.1109/ICIP.2013.6738297
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2013-09-15
Publisher Place	Australia
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Fourier Shift Theorem Confocal Microscopy Zebrafish Maximum Intensity Projection
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in