A framework for generating realistic synthetic sequences of total internal reflection fluorescence microscopy images

Seyed Hamid Rezatofighi; William T.E. Pitkeathly; Stephen Gould; Richard Hartley; Katarina Mele; William E. Hughes; James G. Burchfield

doi:10.1109/ISBI.2013.6556436

A framework for generating realistic synthetic sequences of total internal reflection fluorescence microscopy images

Seyed Hamid Rezatofighi, William T.E. Pitkeathly, Stephen Gould, Richard Hartley, Katarina Mele, William E. Hughes, James G. Burchfield

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

13 Citations (Scopus)

Abstract

Since generation of reliable ground truth annotation of fluorescence microscopy sequences is usually a laborious and expensive task, many proposed detection and tracking methods have been evaluated using synthetic data with known ground truth. However, differences between real and synthetic images may lead to inaccurate judgment about the performance of an algorithm. In this paper, we present a framework for generating realistic synthetic sequences of total internal reflection fluorescence microscope (TIRFM) through simulation of the image formation process and accurate measurement and dynamic models. The sequences generated using this framework appropriately reflect the complexities existing in real TIRFM sequences.

Original language	English
Title of host publication	ISBI 2013 - 2013 IEEE 10th International Symposium on Biomedical Imaging
Subtitle of host publication	From Nano to Macro
Pages	157-160
Number of pages	4
DOIs	https://doi.org/10.1109/ISBI.2013.6556436
Publication status	Published - 2013
Event	2013 IEEE 10th International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2013 - San Francisco, CA, United States Duration: 7 Apr 2013 → 11 Apr 2013

Publication series

Name	Proceedings - International Symposium on Biomedical Imaging
ISSN (Print)	1945-7928
ISSN (Electronic)	1945-8452

Conference

Conference	2013 IEEE 10th International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2013
Country/Territory	United States
City	San Francisco, CA
Period	7/04/13 → 11/04/13

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10.1109/ISBI.2013.6556436

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Rezatofighi, S. H., Pitkeathly, W. T. E., Gould, S., Hartley, R., Mele, K., Hughes, W. E., & Burchfield, J. G. (2013). A framework for generating realistic synthetic sequences of total internal reflection fluorescence microscopy images. In ISBI 2013 - 2013 IEEE 10th International Symposium on Biomedical Imaging: From Nano to Macro (pp. 157-160). Article 6556436 (Proceedings - International Symposium on Biomedical Imaging). https://doi.org/10.1109/ISBI.2013.6556436

Rezatofighi, Seyed Hamid ; Pitkeathly, William T.E. ; Gould, Stephen et al. / A framework for generating realistic synthetic sequences of total internal reflection fluorescence microscopy images. ISBI 2013 - 2013 IEEE 10th International Symposium on Biomedical Imaging: From Nano to Macro. 2013. pp. 157-160 (Proceedings - International Symposium on Biomedical Imaging).

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title = "A framework for generating realistic synthetic sequences of total internal reflection fluorescence microscopy images",

abstract = "Since generation of reliable ground truth annotation of fluorescence microscopy sequences is usually a laborious and expensive task, many proposed detection and tracking methods have been evaluated using synthetic data with known ground truth. However, differences between real and synthetic images may lead to inaccurate judgment about the performance of an algorithm. In this paper, we present a framework for generating realistic synthetic sequences of total internal reflection fluorescence microscope (TIRFM) through simulation of the image formation process and accurate measurement and dynamic models. The sequences generated using this framework appropriately reflect the complexities existing in real TIRFM sequences.",

keywords = "Background estimation, Dynamic model, Synthetic data, TIRFM, Vesicle shape deformation",

author = "Rezatofighi, {Seyed Hamid} and Pitkeathly, {William T.E.} and Stephen Gould and Richard Hartley and Katarina Mele and Hughes, {William E.} and Burchfield, {James G.}",

year = "2013",

doi = "10.1109/ISBI.2013.6556436",

language = "English",

isbn = "9781467364546",

series = "Proceedings - International Symposium on Biomedical Imaging",

pages = "157--160",

booktitle = "ISBI 2013 - 2013 IEEE 10th International Symposium on Biomedical Imaging",

note = "2013 IEEE 10th International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2013 ; Conference date: 07-04-2013 Through 11-04-2013",

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Rezatofighi, SH, Pitkeathly, WTE, Gould, S, Hartley, R, Mele, K, Hughes, WE & Burchfield, JG 2013, A framework for generating realistic synthetic sequences of total internal reflection fluorescence microscopy images. in ISBI 2013 - 2013 IEEE 10th International Symposium on Biomedical Imaging: From Nano to Macro., 6556436, Proceedings - International Symposium on Biomedical Imaging, pp. 157-160, 2013 IEEE 10th International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2013, San Francisco, CA, United States, 7/04/13. https://doi.org/10.1109/ISBI.2013.6556436

A framework for generating realistic synthetic sequences of total internal reflection fluorescence microscopy images. / Rezatofighi, Seyed Hamid; Pitkeathly, William T.E.; Gould, Stephen et al.
ISBI 2013 - 2013 IEEE 10th International Symposium on Biomedical Imaging: From Nano to Macro. 2013. p. 157-160 6556436 (Proceedings - International Symposium on Biomedical Imaging).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AU - Rezatofighi, Seyed Hamid

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AU - Mele, Katarina

AU - Hughes, William E.

AU - Burchfield, James G.

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AB - Since generation of reliable ground truth annotation of fluorescence microscopy sequences is usually a laborious and expensive task, many proposed detection and tracking methods have been evaluated using synthetic data with known ground truth. However, differences between real and synthetic images may lead to inaccurate judgment about the performance of an algorithm. In this paper, we present a framework for generating realistic synthetic sequences of total internal reflection fluorescence microscope (TIRFM) through simulation of the image formation process and accurate measurement and dynamic models. The sequences generated using this framework appropriately reflect the complexities existing in real TIRFM sequences.

KW - Background estimation

KW - Dynamic model

KW - Synthetic data

KW - TIRFM

KW - Vesicle shape deformation

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M3 - Conference contribution

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BT - ISBI 2013 - 2013 IEEE 10th International Symposium on Biomedical Imaging

T2 - 2013 IEEE 10th International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2013

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Rezatofighi SH, Pitkeathly WTE, Gould S, Hartley R, Mele K, Hughes WE et al. A framework for generating realistic synthetic sequences of total internal reflection fluorescence microscopy images. In ISBI 2013 - 2013 IEEE 10th International Symposium on Biomedical Imaging: From Nano to Macro. 2013. p. 157-160. 6556436. (Proceedings - International Symposium on Biomedical Imaging). doi: 10.1109/ISBI.2013.6556436

A framework for generating realistic synthetic sequences of total internal reflection fluorescence microscopy images

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