Dataset Information

Automatic wavelet-based 3D nuclei segmentation and analysis for multicellular embryo quantification.

ABSTRACT: Identification of individual cells in tissues, organs, and in various developing systems is a well-studied problem because it is an essential part of objectively analyzing quantitative images in numerous biological contexts. We developed a size-dependent wavelet-based segmentation method that provides robust segmentation without any preprocessing, filtering or fine-tuning steps, and is robust to the signal-to-noise ratio. The wavelet-based method achieves robust segmentation results with respect to True Positive rate, Precision, and segmentation accuracy compared with other commonly used methods. We applied the segmentation program to zebrafish embryonic development IN TOTO for nuclei segmentation, image registration, and nuclei shape analysis. These new approaches to segmentation provide a means to carry out quantitative patterning analysis with single-cell precision throughout three dimensional tissues and embryos and they have a high tolerance for non-uniform and noisy image data sets.

SUBMITTER: Wu TC

PROVIDER: S-EPMC8110989 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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Automatic wavelet-based 3D nuclei segmentation and analysis for multicellular embryo quantification.

Wu Tzu-Ching TC Wang Xu X Li Linlin L Bu Ye Y Umulis David M DM

Scientific reports 20210510 1

Identification of individual cells in tissues, organs, and in various developing systems is a well-studied problem because it is an essential part of objectively analyzing quantitative images in numerous biological contexts. We developed a size-dependent wavelet-based segmentation method that provides robust segmentation without any preprocessing, filtering or fine-tuning steps, and is robust to the signal-to-noise ratio. The wavelet-based method achieves robust segmentation results with respect ...[more]

PMID: 33972575

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Project description:This paper studies the feasibility of developing an automatic anatomy segmentation (AAS) system in clinical radiology and demonstrates its operation on clinical 3D images.The AAS system, the authors are developing consists of two main parts: object recognition and object delineation. As for recognition, a hierarchical 3D scale-based multiobject method is used for the multiobject recognition task, which incorporates intensity weighted ball-scale (b-scale) information into the active shape model (ASM). For object delineation, an iterative graph-cut-ASM (IGCASM) algorithm is proposed, which effectively combines the rich statistical shape information embodied in ASM with the globally optimal delineation capability of the GC method. The presented IGCASM algorithm is a 3D generalization of the 2D GC-ASM method that they proposed previously in Chen et al. [Proc. SPIE, 7259, 72590C1-72590C-8 (2009)]. The proposed methods are tested on two datasets comprised of images obtained from 20 patients (10 male and 10 female) of clinical abdominal CT scans, and 11 foot magnetic resonance imaging (MRI) scans. The test is for four organs (liver, left and right kidneys, and spleen) segmentation, five foot bones (calcaneus, tibia, cuboid, talus, and navicular). The recognition and delineation accuracies were evaluated separately. The recognition accuracy was evaluated in terms of translation, rotation, and scale (size) error. The delineation accuracy was evaluated in terms of true and false positive volume fractions (TPVF, FPVF). The efficiency of the delineation method was also evaluated on an Intel Pentium IV PC with a 3.4 GHZ CPU machine.The recognition accuracies in terms of translation, rotation, and scale error over all organs are about 8 mm, 10 degrees and 0.03, and over all foot bones are about 3.5709 mm, 0.35 degrees and 0.025, respectively. The accuracy of delineation over all organs for all subjects as expressed in TPVF and FPVF is 93.01% and 0.22%, and all foot bones for all subjects are 93.75% and 0.28%, respectively. While the delineations for the four organs can be accomplished quite rapidly with average of 78 s, the delineations for the five foot bones can be accomplished with average of 70 s.The experimental results showed the feasibility and efficacy of the proposed automatic anatomy segmentation system: (a) the incorporation of shape priors into the GC framework is feasible in 3D as demonstrated previously for 2D images; (b) our results in 3D confirm the accuracy behavior observed in 2D. The hybrid strategy IGCASM seems to be more robust and accurate than ASM and GC individually; and (c) delineations within body regions and foot bones of clinical importance can be accomplished quite rapidly within 1.5 min.

Project description:Objective. The objective of this study is to develop and validate a method for automatically identifying segments of intracranial pressure (ICP) waveform data from external ventricular drainage (EVD) recordings during intermittent drainage and closure.Methods. The proposed method uses time-frequency analysis through wavelets to distinguish periods of ICP waveform in EVD data. By comparing the frequency compositions of the ICP signals (when the EVD system is clamped) and the artifacts (when the system is open), the algorithm can detect short, uninterrupted segments of ICP waveform from the longer periods of non-measurement data. The method involves applying a wavelet transform, calculating the absolute power in a specific range, using Otsu thresholding to automatically identify a threshold, and performing a morphological operation to remove small segments. Two investigators manually graded the same randomly selected one-hour segments of the resulting processed data. Performance metrics were calculated as a percentage.Results. The study analyzed data from 229 patients who had EVD placed following subarachnoid hemorrhage between June 2006 and December 2012. Of these, 155 (67.7%) were female and 62 (27%) developed delayed cerebral ischemia. A total of 45 150 h of data were segmented. 2044 one-hour segments were randomly selected and evaluated by two investigators (MM and DN). Of those, the evaluators agreed on the classification of 1556 one-hour segments. The algorithm was able to correctly identify 86% (1338 h) of ICP waveform data. 8.2% (128 h) of the time the algorithm either partially or fully failed to segment the ICP waveform. 5.4% (84 h) of data, artifacts were mistakenly identified as ICP waveforms (false positives).Conclusion. The proposed algorithm automates the identification of valid ICP waveform segments of waveform in EVD data and thus enables the inclusion in real-time data analysis for decision support. It also standardizes and makes research data management more efficient.

Dataset Information

Automatic wavelet-based 3D nuclei segmentation and analysis for multicellular embryo quantification.

Publications

Automatic wavelet-based 3D nuclei segmentation and analysis for multicellular embryo quantification.

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