Dataset Information

Noise reduction in single time frame optical DNA maps.

ABSTRACT: In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These "fingerprints" of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes. The current solutions to this challenge are computationally rather slow. With high-throughput applications in mind, we here introduce a parameter-free method for filtering a single time frame noisy barcode (snap-shot optical map), measured in a fraction of a second. By using only a single time frame barcode we circumvent the need for post-processing alignment. We demonstrate that our method is successful at providing filtered barcodes which are less noisy and more similar to time averaged barcodes. The method is based on the application of a low-pass filter on a single noisy barcode using the width of the Point Spread Function of the system as a unique, and known, filtering parameter. We find that after applying our method, the Pearson correlation coefficient (a real number in the range from -1 to 1) between the single time-frame barcode and the time average of the aligned kymograph increases significantly, roughly by 0.2 on average. By comparing to a database of more than 3000 theoretical plasmid barcodes we show that the capabilities to identify plasmids is improved by filtering single time-frame barcodes compared to the unfiltered analogues. Since snap-shot experiments and computational time using our method both are less than a second, this study opens up for high throughput optical DNA mapping with improved reproducibility.

SUBMITTER: Torche PC

PROVIDER: S-EPMC5480869 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Noise reduction in single time frame optical DNA maps.

Torche Paola C PC Müller Vilhelm V Westerlund Fredrik F Ambjörnsson Tobias T

PloS one 20170622 6

In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These "fingerprints" of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align d ...[more]

PMID: 28640821

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Project description:BackgroundQuantum noise intrinsically limits the quality of fluoroscopic images. The lower is the X-ray dose the higher is the noise. Fluoroscopy video processing can enhance image quality and allows further patient's dose lowering. This study aims to assess the performances achieved by a Noise Variance Conditioned Average (NVCA) spatio-temporal filter for real-time denoising of fluoroscopic sequences. The filter is specifically designed for quantum noise suppression and edge preservation. It is an average filter that excludes neighborhood pixel values exceeding noise statistic limits, by means of a threshold which depends on the local noise standard deviation, to preserve the image spatial resolution. The performances were evaluated in terms of contrast-to-noise-ratio (CNR) increment, image blurring (full width of the half maximum of the line spread function) and computational time. The NVCA filter performances were compared to those achieved by simple moving average filters and the state-of-the-art video denoising block matching-4D (VBM4D) algorithm. The influence of the NVCA filter size and threshold on the final image quality was evaluated too.ResultsFor NVCA filter mask size of 5 × 5 × 5 pixels (the third dimension represents the temporal extent of the filter) and a threshold level equal to 2 times the local noise standard deviation, the NVCA filter achieved a 10% increase of the CNR with respect to the unfiltered sequence, while the VBM4D achieved a 14% increase. In the case of NVCA, the edge blurring did not depend on the speed of the moving objects; on the other hand, the spatial resolution worsened of about 2.2 times by doubling the objects speed with VBM4D. The NVCA mask size and the local noise-threshold level are critical for final image quality. The computational time of the NVCA filter was found to be just few percentages of that required for the VBM4D filter.ConclusionsThe NVCA filter obtained a better image quality compared to simple moving average filters, and a lower but comparable quality when compared with the VBM4D filter. The NVCA filter showed to preserve edge sharpness, in particular in the case of moving objects (performing even better than VBM4D). The simplicity of the NVCA filter and its low computational burden make this filter suitable for real-time video processing and its hardware implementation is ready to be included in future fluoroscopy devices, offering further lowering of patient's X-ray dose.

Dataset Information

Noise reduction in single time frame optical DNA maps.

Publications

Noise reduction in single time frame optical DNA maps.

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