Automatic noise quantification for confocal fluorescence microscopy images

Paul, Perrine; Duessmann, Heiko; Bernaś, Tytus; Huber, Heinrich J.; Kalamatianos, Dimitrios

doi:10.1016/j.compmedimag.2010.04.001

Cited by 14 publications

(12 citation statements)

References 12 publications

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“…S1 B) and moving cells were identified as having an absolute value greater than 6 x the estimated standard deviation of the image’s white noise (Fig. S1 C; Paul et al, 2010). Cells larger than 5 μm 2 were then consecutively morphologically dilated and eroded, using structuring disks of radii 41 μηι and 21 μηι, respectively.…”

Section: Methodsmentioning

confidence: 99%

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Histological and haematological analysis of the ascidianBotrylloides leachii(Savigny, 1816) during whole-body regeneration

Blanchoud

Zondag

Lamare

et al. 2017

Preprint

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(250 words)Whole-body regeneration, the formation of an entire adult from only a small fragment of its own tissue, is extremely rare among chordates. Exceptionally, in the colonial ascidianBotrylloides leachii, a fully functional adult is formed from their common vascular system, upon ablation of all adults from the colony, in just 10 days thanks to their high blastogenetic potential. While previous studies have identified key genetic markers and morphological changes, no study has yet focused on the haematological aspects of regeneration despite the major involvement of the remaining vascular system and the contained haemocytes in this process. To dissect this process, we analysed colony blood flow patterns using time-lapse microscopy to obtain a quantitative description of the velocity, reversal pattern, and average distance travelled by haemocytes. We also observed that flows present during regeneration are powered by temporally and spatially synchronized contractions of the terminal ampullae. In addition, we revised previous studies onB.leachiihaematology as well as asexual development using histological sectioning, and compared the role of haemocytes during whole-body regeneration. We found that regeneration starts with a rapid healing response characterized by blood clotting and infiltration of immunocytes, followed by increased activity of haemoblasts, recruitment of macrophage-like cells for clearing the tissues of debris, and their subsequent disappearance from the circulation concomitant with the maturation of a single regenerated adult. Overall, we provide a uniquely detailed account of the haematological properties of regeneratingB.leachiicolonies, providing novel lines of inquiry towards the decipherment of regeneration in chordates.

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Section: Methodsmentioning

confidence: 99%

“…We first identified ampullae in every frame (Fig. S2 A) as regions darker than 20 x the estimated standard deviation of the image’s white noise (Paul et al, 2010). The resulting binarized image was then consecutively morphologically opened and closed, using a structuring disk of radius 9.5 μm (Fig.…”

Section: Methodsmentioning

confidence: 99%

Histological and haematological analysis of the ascidianBotrylloides leachii(Savigny, 1816) during whole-body regeneration

Blanchoud

Zondag

Lamare

et al. 2017

Preprint

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“…As the first step towards segmentation, a background subtraction (as described in 2.1) can be applied, here affecting only this step of the analysis. Second, default de-noising is performed by applying a Gaussian filter with a radius of 0.6 px [59] and by subtracting the estimated mean of the uniform Gaussian white noise, replacing the homogeneity analyzer proposed in [60,61], which is utilized to identify the empty portions of the image, by the Absolute Difference Mask (ADM) edge detector [62]. Candidate object locations are then detected using the ''à trous'' wavelet transform [30], followed by a filtering step in which only single-pixel local maxima detections are kept.…”

Section: Image Segmentationmentioning

confidence: 99%

CAST: An automated segmentation and tracking tool for the analysis of transcriptional kinetics from single-cell time-lapse recordings

Blanchoud

Nicolas

Zoller

et al. 2015

Methods

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“…Then, the problem is addressed by using a simple regression based approach. In [11] authors show that the scale parameter of Poisson noise is not a pure estimate of the detector gain. In this work, a maximum likelihood method is proposed which sometimes leads to inaccurate results, due to an unreliable background classification scheme.…”

Section: Introductionmentioning

confidence: 97%

“…Previous noise parameter estimation studies in fluorescence imaging systems can be found in [7,8,9,10,11,12]. The author in [7] proposes a cumulantbased approach.…”

Section: Introductionmentioning

confidence: 99%

Poisson-Gaussian noise parameter estimation in fluorescence microscopy imaging

Jezierska

Talbot

Chaux

et al. 2012

2012 9th IEEE International Symposium on Biomedical Imaging (ISBI)

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In this paper, we present a new fully automatic approach for noise parameter estimation in the context of fluorescence imaging systems. In particular, we address the problem of Poisson-Gaussian noise modeling in the nonstationary case. In microscopy practice, the nonstationarity is due to the photobleaching effect. The proposed method consists of an adequate moment based initialization followed by Expectation-Maximization iterations. This approach is shown to provide reliable estimates of the mean and the variance of the Gaussian noise and of the scale parameter of Poisson noise, as well as of the photobleaching rates. The algorithm performance is demonstrated on both synthetic and real macro confocal laser scanning microscope image sequences.

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Automatic noise quantification for confocal fluorescence microscopy images

Cited by 14 publications

References 12 publications

Histological and haematological analysis of the ascidianBotrylloides leachii(Savigny, 1816) during whole-body regeneration

Histological and haematological analysis of the ascidianBotrylloides leachii(Savigny, 1816) during whole-body regeneration

CAST: An automated segmentation and tracking tool for the analysis of transcriptional kinetics from single-cell time-lapse recordings

Poisson-Gaussian noise parameter estimation in fluorescence microscopy imaging

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