Title: PhytoOracle: Scalable, modular phenomics data processing pipelines
As phenomics data volume and dimensionality increase due to advancements in sensor technology, there is an urgent need to develop and implement scalable data processing pipelines. Current phenomics data processing pipelines lack modularity, extensibility, and processing distribution across sensor modalities and phenotyping platforms. To address these challenges, we developed PhytoOracle (PO), a suite of modular, scalable pipelines for processing large volumes of field phenomics RGB, thermal, PSII chlorophyll fluorescence 2D images, and 3D point clouds. PhytoOracle aims to ( i ) improve data processing efficiency; ( ii ) provide an extensible, reproducible computing framework; and ( iii ) enable data fusion of multi-modal phenomics data. PhytoOracle integrates open-source distributed computing frameworks for parallel processing on high-performance computing, cloud, and local computing environments. Each pipeline component is available as a standalone container, providing transferability, extensibility, and reproducibility. The PO pipeline extracts and associates individual plant traits across sensor modalities and collection time points, representing a unique multi-system approach to addressing the genotype-phenotype gap. To date, PO supports lettuce and sorghum phenotypic trait extraction, with a goal of widening the range of supported species in the future. At the maximum number of cores tested in this study (1,024 cores), PO processing times were: 235 minutes for 9,270 RGB images (140.7 GB), 235 minutes for 9,270 thermal images (5.4 GB), and 13 minutes for 39,678 PSII images (86.2 GB). These processing times represent end-to-end processing, from raw data to fully processed numerical phenotypic trait data. Repeatability values of 0.39-0.95 (bounding area), 0.81-0.95 (axis-aligned bounding volume), 0.79-0.94 (oriented bounding volume), 0.83-0.95 (plant height), and 0.81-0.95 (number of points) were observed in Field Scanalyzer data. We also show the ability of PO to process drone data with a repeatability of 0.55-0.95 (bounding area). more »« less
Abstract Real-time execution of machine learning (ML) pipelines on radiology images is difficult due to limited computing resources in clinical environments, whereas running them in research clusters requires efficient data transfer capabilities. We developed Niffler, an open-source Digital Imaging and Communications in Medicine (DICOM) framework that enables ML and processing pipelines in research clusters by efficiently retrieving images from the hospitals’ PACS and extracting the metadata from the images. We deployed Niffler at our institution (Emory Healthcare, the largest healthcare network in the state of Georgia) and retrieved data from 715 scanners spanning 12 sites, up to 350 GB/day continuously in real-time as a DICOM data stream over the past 2 years. We also used Niffler to retrieve images bulk on-demand based on user-provided filters to facilitate several research projects. This paper presents the architecture and three such use cases of Niffler. First, we executed an IVC filter detection and segmentation pipeline on abdominal radiographs in real-time, which was able to classify 989 test images with an accuracy of 96.0%. Second, we applied the Niffler Metadata Extractor to understand the operational efficiency of individual MRI systems based on calculated metrics. We benchmarked the accuracy of the calculated exam time windows by comparing Niffler against the Clinical Data Warehouse (CDW). Niffler accurately identified the scanners’ examination timeframes and idling times, whereas CDW falsely depicted several exam overlaps due to human errors. Third, with metadata extracted from the images by Niffler, we identified scanners with misconfigured time and reconfigured five scanners. Our evaluations highlight how Niffler enables real-time ML and processing pipelines in a research cluster.
Kumar, Nilay; Huizar, Francisco J.; Farfán-Pira, Keity J.; Brodskiy, Pavel A.; Soundarrajan, Dharsan K.; Nahmad, Marcos; Zartman, Jeremiah J.(
, Frontiers in Genetics)
Phenomics requires quantification of large volumes of image data, necessitating high throughput image processing approaches. Existing image processing pipelines for Drosophila wings, a powerful genetic model for studying the underlying genetics for a broad range of cellular and developmental processes, are limited in speed, precision, and functional versatility. To expand on the utility of the wing as a phenotypic screening system, we developed MAPPER, an automated machine learning-based pipeline that quantifies high-dimensional phenotypic signatures, with each dimension quantifying a unique morphological feature of the Drosophila wing. MAPPER magnifies the power of Drosophila phenomics by rapidly quantifying subtle phenotypic differences in sample populations. We benchmarked MAPPER’s accuracy and precision in replicating manual measurements to demonstrate its widespread utility. The morphological features extracted using MAPPER reveal variable sexual dimorphism across Drosophila species and unique underlying sex-specific differences in morphogen signaling in male and female wings. Moreover, the length of the proximal-distal axis across the species and sexes shows a conserved scaling relationship with respect to the wing size. In sum, MAPPER is an open-source tool for rapid, high-dimensional analysis of large imaging datasets. These high-content phenomic capabilities enable rigorous and systematic identification of genotype-to-phenotype relationships in a broad range of screening and drug testing applications and amplify the potential power of multimodal genomic approaches.
Evolution has honed predatory skills in the natural world where localizing and intercepting fast-moving prey is required. The current generation of robotic systems mimics these biological systems using deep learning. High-speed processing of the camera frames using convolutional neural networks (CNN) (frame pipeline) on such constrained aerial edge-robots gets resource-limited. Adding more compute resources also eventually limits the throughput at the frame rate of the camera as frame-only traditional systems fail to capture the detailed temporal dynamics of the environment. Bio-inspired event cameras and spiking neural networks (SNN) provide an asynchronous sensor-processor pair (event pipeline) capturing the continuous temporal details of the scene for high-speed but lag in terms of accuracy. In this work, we propose a target localization system combining event-camera and SNN-based high-speed target estimation and frame-based camera and CNN-driven reliable object detection by fusing complementary spatio-temporal prowess of event and frame pipelines. One of our main contributions involves the design of an SNN filter that borrows from the neural mechanism for ego-motion cancelation in houseflies. It fuses the vestibular sensors with the vision to cancel the activity corresponding to the predator's self-motion. We also integrate the neuro-inspired multi-pipeline processing with task-optimized multi-neuronal pathway structure in primates and insects. The system is validated to outperform CNN-only processing using prey-predator drone simulations in realistic 3D virtual environments. The system is then demonstrated in a real-world multi-drone set-up with emulated event data. Subsequently, we use recorded actual sensory data from multi-camera and inertial measurement unit (IMU) assembly to show desired working while tolerating the realistic noise in vision and IMU sensors. We analyze the design space to identify optimal parameters for spiking neurons, CNN models, and for checking their effect on the performance metrics of the fused system. Finally, we map the throughput controlling SNN and fusion network on edge-compatible Zynq-7000 FPGA to show a potential 264 outputs per second even at constrained resource availability. This work may open new research directions by coupling multiple sensing and processing modalities inspired by discoveries in neuroscience to break fundamental trade-offs in frame-based computer vision 1 .
The PoseASL dataset consists of color and depth videos collected from ASL signers at the Linguistic and Assistive Technologies Laboratory under the direction of Matt Huenerfauth, as part of a collaborative research project with researchers at the Rochester Institute of Technology, Boston University, and the University of Pennsylvania. Access: After becoming an authorized user of Databrary, please contact Matt Huenerfauth if you have difficulty accessing this volume. We have collected a new dataset consisting of color and depth videos of fluent American Sign Language signers performing sequences ASL signs and sentences. Given interest among sign-recognition and other computer-vision researchers in red-green-blue-depth (RBGD) video, we release this dataset for use by the research community. In addition to the video files, we share depth data files from a Kinect v2 sensor, as well as additional motion-tracking files produced through post-processing of this data. Organization of the Dataset: The dataset is organized into sub-folders, with codenames such as "P01" or "P16" etc. These codenames refer to specific human signers who were recorded in this dataset. Please note that there was no participant P11 nor P14; those numbers were accidentally skipped during the process of making appointments to collect video stimuli. Task: During the recording session, the participant was met by a member of our research team who was a native ASL signer. No other individuals were present during the data collection session. After signing the informed consent and video release document, participants responded to a demographic questionnaire. Next, the data-collection session consisted of English word stimuli and cartoon videos. The recording session began with showing participants stimuli consisting of slides that displayed English word and photos of items, and participants were asked to produce the sign for each (PDF included in materials subfolder). Next, participants viewed three videos of short animated cartoons, which they were asked to recount in ASL: - Canary Row, Warner Brothers Merrie Melodies 1950 (the 7-minute video divided into seven parts) - Mr. Koumal Flies Like a Bird, Studio Animovaneho Filmu 1969 - Mr. Koumal Battles his Conscience, Studio Animovaneho Filmu 1971 The word list and cartoons were selected as they are identical to the stimuli used in the collection of the Nicaraguan Sign Language video corpora - see: Senghas, A. (1995). Children’s Contribution to the Birth of Nicaraguan Sign Language. Doctoral dissertation, Department of Brain and Cognitive Sciences, MIT. Demographics: All 14 of our participants were fluent ASL signers. As screening, we asked our participants: Did you use ASL at home growing up, or did you attend a school as a very young child where you used ASL? All the participants responded affirmatively to this question. A total of 14 DHH participants were recruited on the Rochester Institute of Technology campus. Participants included 7 men and 7 women, aged 21 to 35 (median = 23.5). All of our participants reported that they began using ASL when they were 5 years old or younger, with 8 reporting ASL use since birth, and 3 others reporting ASL use since age 18 months. Filetypes: *.avi, *_dep.bin: The PoseASL dataset has been captured by using a Kinect 2.0 RGBD camera. The output of this camera system includes multiple channels which include RGB, depth, skeleton joints (25 joints for every video frame), and HD face (1,347 points). The video resolution produced in 1920 x 1080 pixels for the RGB channel and 512 x 424 pixels for the depth channels respectively. Due to limitations in the acceptable filetypes for sharing on Databrary, it was not permitted to share binary *_dep.bin files directly produced by the Kinect v2 camera system on the Databrary platform. If your research requires the original binary *_dep.bin files, then please contact Matt Huenerfauth. *_face.txt, *_HDface.txt, *_skl.txt: To make it easier for future researchers to make use of this dataset, we have also performed some post-processing of the Kinect data. To extract the skeleton coordinates of the RGB videos, we used the Openpose system, which is capable of detecting body, hand, facial, and foot keypoints of multiple people on single images in real time. The output of Openpose includes estimation of 70 keypoints for the face including eyes, eyebrows, nose, mouth and face contour. The software also estimates 21 keypoints for each of the hands (Simon et al, 2017), including 3 keypoints for each finger, as shown in Figure 2. Additionally, there are 25 keypoints estimated for the body pose (and feet) (Cao et al, 2017; Wei et al, 2016). Reporting Bugs or Errors: Please contact Matt Huenerfauth to report any bugs or errors that you identify in the corpus. We appreciate your help in improving the quality of the corpus over time by identifying any errors. Acknowledgement: This material is based upon work supported by the National Science Foundation under award 1749376: "Collaborative Research: Multimethod Investigation of Articulatory and Perceptual Constraints on Natural Language Evolution."
Raut, Bhupendra A.; Muradyan, Paytsar; Sankaran, Rajesh; Jackson, Robert C.; Park, Seongha; Shahkarami, Sean A.; Dematties, Dario; Kim, Yongho; Swantek, Joseph; Conrad, Neal; et al(
, Atmospheric Measurement Techniques)
Abstract. Phase correlation (PC) is a well-known method for estimating cloud motion vectors (CMVs) from infrared and visible spectrum images. Commonly, phase shift is computed in the small blocks of the images using the fast Fourier transform. In this study, we investigate the performance and the stability of the blockwise PC method by changing the block size, the frame interval, and combinations of red, green, and blue (RGB) channels from the total sky imager (TSI) at the United States Atmospheric Radiation Measurement user facility's Southern Great Plains site. We find that shorter frame intervals, followed by larger block sizes, are responsible for stable estimates of the CMV, as suggested by the higher autocorrelations. The choice of RGB channels has a limited effect on the quality of CMVs, and the red and the grayscale images are marginally more reliable than the other combinations during rapidly evolving low-level clouds. The stability of CMVs was tested at different image resolutions with an implementation of the optimized algorithm on the Sage cyberinfrastructure test bed. We find that doubling the frame rate outperforms quadrupling the image resolution in achieving CMV stability. The correlations of CMVs with the wind data are significant in the range of 0.38–0.59 with a 95 % confidence interval, despite the uncertainties and limitations of both datasets. A comparison of the PC method with constructed data and the optical flow method suggests that the post-processing of the vector field has a significant effect on the quality of the CMV. The raindrop-contaminated images can be identified by the rotation of the TSI mirror in the motion field. The results of this study are critical to optimizing algorithms for edge-computing sensor systems.
@article{osti_10412983,
place = {Country unknown/Code not available},
title = {PhytoOracle: Scalable, modular phenomics data processing pipelines},
url = {https://par.nsf.gov/biblio/10412983},
DOI = {10.3389/fpls.2023.1112973},
abstractNote = {As phenomics data volume and dimensionality increase due to advancements in sensor technology, there is an urgent need to develop and implement scalable data processing pipelines. Current phenomics data processing pipelines lack modularity, extensibility, and processing distribution across sensor modalities and phenotyping platforms. To address these challenges, we developed PhytoOracle (PO), a suite of modular, scalable pipelines for processing large volumes of field phenomics RGB, thermal, PSII chlorophyll fluorescence 2D images, and 3D point clouds. PhytoOracle aims to ( i ) improve data processing efficiency; ( ii ) provide an extensible, reproducible computing framework; and ( iii ) enable data fusion of multi-modal phenomics data. PhytoOracle integrates open-source distributed computing frameworks for parallel processing on high-performance computing, cloud, and local computing environments. Each pipeline component is available as a standalone container, providing transferability, extensibility, and reproducibility. The PO pipeline extracts and associates individual plant traits across sensor modalities and collection time points, representing a unique multi-system approach to addressing the genotype-phenotype gap. To date, PO supports lettuce and sorghum phenotypic trait extraction, with a goal of widening the range of supported species in the future. At the maximum number of cores tested in this study (1,024 cores), PO processing times were: 235 minutes for 9,270 RGB images (140.7 GB), 235 minutes for 9,270 thermal images (5.4 GB), and 13 minutes for 39,678 PSII images (86.2 GB). These processing times represent end-to-end processing, from raw data to fully processed numerical phenotypic trait data. Repeatability values of 0.39-0.95 (bounding area), 0.81-0.95 (axis-aligned bounding volume), 0.79-0.94 (oriented bounding volume), 0.83-0.95 (plant height), and 0.81-0.95 (number of points) were observed in Field Scanalyzer data. We also show the ability of PO to process drone data with a repeatability of 0.55-0.95 (bounding area).},
journal = {Frontiers in Plant Science},
volume = {14},
author = {Gonzalez, Emmanuel M. and Zarei, Ariyan and Hendler, Nathanial and Simmons, Travis and Zarei, Arman and Demieville, Jeffrey and Strand, Robert and Rozzi, Bruno and Calleja, Sebastian and Ellingson, Holly and Cosi, Michele and Davey, Sean and Lavelle, Dean O. and Truco, Maria José and Swetnam, Tyson L. and Merchant, Nirav and Michelmore, Richard W. and Lyons, Eric and Pauli, Duke},
}
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