‘miSimBa’ — A simulator of synthetic time-lapsed microscopy images of bacterial cells

Leonardo Martins, Jose Fonseca, Andre Ribeiro

Research output: Contribution to conferenceOther

5 Citations (Scopus)

Abstract

Escherichia coli is a model organism for the study of multiple biological processes, including gene expression and cellular aging. Recently, these studies started to rely on temporal single cell imaging. To support these efforts, available automated image analysis methods should be improved. One important step is their validation. Ideally, the 'ground truth' of the images should be known, which is possible only in synthetic images. To simulate artificial images of E. coli cells, we are developing the 'miSimBa' tool (Microscopy Image Simulator of Bacterial Cells). 'miSimBa' simulates images that reproduce the spatial and temporal bacterial organization by modelling realistically cell morphology (shape, size and spatial arrangement), cell growth and division, cell motility and some internal functions and intracellular structures, namely, the nucleoid. This tool also incorporates image acquisition parameters that simulate illumination and the primary sources of noise.
Original languageEnglish
Pages1-6
Number of pages6
DOIs
Publication statusPublished - Feb 2015
Event2015 IEEE 4th Portuguese Meeting on Bioengineering (ENBENG) - Porto, Portugal
Duration: 26 Feb 201528 Feb 2015

Conference

Conference2015 IEEE 4th Portuguese Meeting on Bioengineering (ENBENG)
Period26/02/1528/02/15

Fingerprint

Microscopy
Escherichia coli
Biological Phenomena
Cell Shape
Cell Aging
Lighting
Cell Division
Cell Movement
Noise
Gene Expression
Growth

Cite this

Martins, L., Fonseca, J., & Ribeiro, A. (2015). ‘miSimBa’ — A simulator of synthetic time-lapsed microscopy images of bacterial cells. 1-6. 2015 IEEE 4th Portuguese Meeting on Bioengineering (ENBENG), . https://doi.org/10.1109/ENBENG.2015.7088854
Martins, Leonardo ; Fonseca, Jose ; Ribeiro, Andre. / ‘miSimBa’ — A simulator of synthetic time-lapsed microscopy images of bacterial cells. 2015 IEEE 4th Portuguese Meeting on Bioengineering (ENBENG), .6 p.
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Martins, L, Fonseca, J & Ribeiro, A 2015, '‘miSimBa’ — A simulator of synthetic time-lapsed microscopy images of bacterial cells' 2015 IEEE 4th Portuguese Meeting on Bioengineering (ENBENG), 26/02/15 - 28/02/15, pp. 1-6. https://doi.org/10.1109/ENBENG.2015.7088854

‘miSimBa’ — A simulator of synthetic time-lapsed microscopy images of bacterial cells. / Martins, Leonardo; Fonseca, Jose; Ribeiro, Andre.

2015. 1-6 2015 IEEE 4th Portuguese Meeting on Bioengineering (ENBENG), .

Research output: Contribution to conferenceOther

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AB - Escherichia coli is a model organism for the study of multiple biological processes, including gene expression and cellular aging. Recently, these studies started to rely on temporal single cell imaging. To support these efforts, available automated image analysis methods should be improved. One important step is their validation. Ideally, the 'ground truth' of the images should be known, which is possible only in synthetic images. To simulate artificial images of E. coli cells, we are developing the 'miSimBa' tool (Microscopy Image Simulator of Bacterial Cells). 'miSimBa' simulates images that reproduce the spatial and temporal bacterial organization by modelling realistically cell morphology (shape, size and spatial arrangement), cell growth and division, cell motility and some internal functions and intracellular structures, namely, the nucleoid. This tool also incorporates image acquisition parameters that simulate illumination and the primary sources of noise.

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