Dataset Information

DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning.

ABSTRACT: Microscopy image analysis is a major bottleneck in quantification of single-cell microscopy data, typically requiring human oversight and curation, which limit both accuracy and throughput. To address this, we developed a deep learning-based image analysis pipeline that performs segmentation, tracking, and lineage reconstruction. Our analysis focuses on time-lapse movies of Escherichia coli cells trapped in a "mother machine" microfluidic device, a scalable platform for long-term single-cell analysis that is widely used in the field. While deep learning has been applied to cell segmentation problems before, our approach is fundamentally innovative in that it also uses machine learning to perform cell tracking and lineage reconstruction. With this framework we are able to get high fidelity results (1% error rate), without human intervention. Further, the algorithm is fast, with complete analysis of a typical frame containing ~150 cells taking <700msec. The framework is not constrained to a particular experimental set up and has the potential to generalize to time-lapse images of other organisms or different experimental configurations. These advances open the door to a myriad of applications including real-time tracking of gene expression and high throughput analysis of strain libraries at single-cell resolution.

SUBMITTER: Lugagne JB

PROVIDER: S-EPMC7153852 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Publications

DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning.

Lugagne Jean-Baptiste JB Lin Haonan H Dunlop Mary J MJ

PLoS computational biology 20200413 4

Microscopy image analysis is a major bottleneck in quantification of single-cell microscopy data, typically requiring human oversight and curation, which limit both accuracy and throughput. To address this, we developed a deep learning-based image analysis pipeline that performs segmentation, tracking, and lineage reconstruction. Our analysis focuses on time-lapse movies of Escherichia coli cells trapped in a "mother machine" microfluidic device, a scalable platform for long-term single-cell ana ...[more]

PMID: 32282792

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Project description:Tissue phase mapping (TPM) is an MRI technique for quantification of regional biventricular myocardial velocities. Despite its potential, clinical use is limited due to the requisite labor-intensive manual segmentation of cardiac contours for all time frames. The purpose of this study was to develop a deep learning (DL) network for automated segmentation of TPM images, without significant loss in segmentation and myocardial velocity quantification accuracy compared with manual segmentation. We implemented a multi-channel 3D (three dimensional; 2D + time) dense U-Net that trained on magnitude and phase images and combined cross-entropy, Dice, and Hausdorff distance loss terms to improve the segmentation accuracy and suppress unnatural boundaries. The dense U-Net was trained and tested with 150 multi-slice, multi-phase TPM scans (114 scans for training, 36 for testing) from 99 heart transplant patients (44 females, 1-4 scans/patient), where the magnitude and velocity-encoded (Vx , Vy , Vz ) images were used as input and the corresponding manual segmentation masks were used as reference. The accuracy of DL segmentation was evaluated using quantitative metrics (Dice scores, Hausdorff distance) and linear regression and Bland-Altman analyses on the resulting peak radial and longitudinal velocities (Vr and Vz ). The mean segmentation time was about 2 h per patient for manual and 1.9 ± 0.3 s for DL. Our network produced good accuracy (median Dice = 0.85 for left ventricle (LV), 0.64 for right ventricle (RV), Hausdorff distance = 3.17 pixels) compared with manual segmentation. Peak Vr and Vz measured from manual and DL segmentations were strongly correlated (R ≥ 0.88) and in good agreement with manual analysis (mean difference and limits of agreement for Vz and Vr were -0.05 ± 0.98 cm/s and -0.06 ± 1.18 cm/s for LV, and -0.21 ± 2.33 cm/s and 0.46 ± 4.00 cm/s for RV, respectively). The proposed multi-channel 3D dense U-Net was capable of reducing the segmentation time by 3,600-fold, without significant loss in accuracy in tissue velocity measurements.

Project description:BackgroundComposition of tissue types within a wound is a useful indicator of its healing progression. Tissue composition is clinically used in wound healing tools (eg, Bates-Jensen Wound Assessment Tool) to assess risk and recommend treatment. However, wound tissue identification and the estimation of their relative composition is highly subjective. Consequently, incorrect assessments could be reported, leading to downstream impacts including inappropriate dressing selection, failure to identify wounds at risk of not healing, or failure to make appropriate referrals to specialists.ObjectiveThis study aimed to measure inter- and intrarater variability in manual tissue segmentation and quantification among a cohort of wound care clinicians and determine if an objective assessment of tissue types (ie, size and amount) can be achieved using deep neural networks.MethodsA data set of 58 anonymized wound images of various types of chronic wounds from Swift Medical's Wound Database was used to conduct the inter- and intrarater agreement study. The data set was split into 3 subsets with 50% overlap between subsets to measure intrarater agreement. In this study, 4 different tissue types (epithelial, granulation, slough, and eschar) within the wound bed were independently labeled by the 5 wound clinicians at 1-week intervals using a browser-based image annotation tool. In addition, 2 deep convolutional neural network architectures were developed for wound segmentation and tissue segmentation and were used in sequence in the workflow. These models were trained using 465,187 and 17,000 image-label pairs, respectively. This is the largest and most diverse reported data set used for training deep learning models for wound and wound tissue segmentation. The resulting models offer robust performance in diverse imaging conditions, are unbiased toward skin tones, and could execute in near real time on mobile devices.ResultsA poor to moderate interrater agreement in identifying tissue types in chronic wound images was reported. A very poor Krippendorff α value of .014 for interrater variability when identifying epithelization was observed, whereas granulation was most consistently identified by the clinicians. The intrarater intraclass correlation (3,1), however, indicates that raters were relatively consistent when labeling the same image multiple times over a period. Our deep learning models achieved a mean intersection over union of 0.8644 and 0.7192 for wound and tissue segmentation, respectively. A cohort of wound clinicians, by consensus, rated 91% (53/58) of the tissue segmentation results to be between fair and good in terms of tissue identification and segmentation quality.ConclusionsThe interrater agreement study validates that clinicians exhibit considerable variability when identifying and visually estimating wound tissue proportion. The proposed deep learning technique provides objective tissue identification and measurements to assist clinicians in documenting the wound more accurately and could have a significant impact on wound care when deployed at scale.

Dataset Information

DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning.

Publications

DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning.

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