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Tytuł pozycji:

Visual4DTracker: a tool to interact with 3D + t image stacks.

Tytuł:
Visual4DTracker: a tool to interact with 3D + t image stacks.
Autorzy:
Cordelli E; Unit of Computer Systems and Bioinformatics, Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy. .
Soda P; Unit of Computer Systems and Bioinformatics, Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy.
Iannello G; Unit of Computer Systems and Bioinformatics, Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy.
Źródło:
BMC bioinformatics [BMC Bioinformatics] 2021 Feb 08; Vol. 22 (1), pp. 53. Date of Electronic Publication: 2021 Feb 08.
Typ publikacji:
Journal Article
Język:
English
Imprint Name(s):
Original Publication: [London] : BioMed Central, 2000-
MeSH Terms:
Algorithms*
Image Processing, Computer-Assisted*
Imaging, Three-Dimensional*
Software*
Microscopy
References:
Mutat Res. 2013 Jan-Mar;752(1):10-24. (PMID: 22940039)
Nature. 2010 Apr 1;464(7289):721-7. (PMID: 20360735)
Mol Aspects Med. 2016 Jun;49:49-77. (PMID: 27012748)
J Cell Sci. 2009 Mar 15;122(Pt 6):753-67. (PMID: 19261845)
Dev Cell. 2015 Mar 23;32(6):678-92. (PMID: 25752962)
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Free Radic Res. 2016 Nov;50(sup1):S40-S50. (PMID: 27593084)
Diabetes. 2011 Nov;60(11):2830-42. (PMID: 21896929)
Methods. 2017 Feb 15;115:80-90. (PMID: 27713081)
IEEE Trans Pattern Anal Mach Intell. 1979 Feb;1(2):224-7. (PMID: 21868852)
Langmuir. 2006 May 9;22(10):4710-9. (PMID: 16649786)
Methods Cell Biol. 2014;123:193-215. (PMID: 24974029)
Contributed Indexing:
Keywords: Blobs; Image proofreading; MATLAB package; Tracking
Entry Date(s):
Date Created: 20210209 Date Completed: 20210217 Latest Revision: 20220219
Update Code:
20240104
PubMed Central ID:
PMC7869512
DOI:
10.1186/s12859-020-03820-y
PMID:
33557754
Czasopismo naukowe
Background: Biological phenomena usually evolves over time and recent advances in high-throughput microscopy have made possible to collect multiple 3D images over time, generating [Formula: see text] (or 4D) datasets. To extract useful information there is the need to extract spatial and temporal data on the particles that are in the images, but particle tracking and feature extraction need some kind of assistance.
Results: This manuscript introduces our new freely downloadable toolbox, the Visual4DTracker. It is a MATLAB package implementing several useful functionalities to navigate, analyse and proof-read the track of each particle detected in any [Formula: see text] stack. Furthermore, it allows users to proof-read and to evaluate the traces with respect to a given gold standard. The Visual4DTracker toolbox permits the users to visualize and save all the generated results through a user-friendly graphical user interface. This tool has been successfully used in three applicative examples. The first processes synthetic data to show all the software functionalities. The second shows how to process a 4D image stack showing the time-lapse growth of Drosophila cells in an embryo. The third example presents the quantitative analysis of insulin granules in living beta-cells, showing that such particles have two main dynamics that coexist inside the cells.
Conclusions: Visual4DTracker is a software package for MATLAB to visualize, handle and manually track [Formula: see text] stacks of microscopy images containing objects such cells, granules, etc.. With its unique set of functions, it remarkably permits the user to analyze and proof-read 4D data in a friendly 3D fashion. The tool is freely available at https://drive.google.com/drive/folders/19AEn0TqP-2B8Z10kOavEAopTUxsKUV73?usp=sharing.
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