scholarly journals Image Harvest: an open-source platform for high-throughput plant image processing and analysis

2016 ◽  
Vol 67 (11) ◽  
pp. 3587-3599 ◽  
Author(s):  
Avi C. Knecht ◽  
Malachy T. Campbell ◽  
Adam Caprez ◽  
David R. Swanson ◽  
Harkamal Walia
2017 ◽  
Author(s):  
Jose C. Tovar ◽  
J. Steen Hoyer ◽  
Andy Lin ◽  
Allison Tielking ◽  
Monica Tessman ◽  
...  

ABSTRACTPremise of the study: Image-based phenomics is a powerful approach to capture and quantify plant diversity. However, commercial platforms that make consistent image acquisition easy are often cost-prohibitive. To make high-throughput phenotyping methods more accessible, low-cost microcomputers and cameras can be used to acquire plant image data.Methods and Results: We used low-cost Raspberry Pi computers and cameras to manage and capture plant image data. Detailed here are three different applications of Raspberry Pi controlled imaging platforms for seed and shoot imaging. Images obtained from each platform were suitable for extracting quantifiable plant traits (shape, area, height, color) en masse using open-source image processing software such as PlantCV.Conclusion: This protocol describes three low-cost platforms for image acquisition that are useful for quantifying plant diversity. When coupled with open-source image processing tools, these imaging platforms provide viable low-cost solutions for incorporating high-throughput phenomics into a wide range of research programs.


Sensors ◽  
2021 ◽  
Vol 21 (11) ◽  
pp. 3691
Author(s):  
Ciprian Orhei ◽  
Silviu Vert ◽  
Muguras Mocofan ◽  
Radu Vasiu

Computer Vision is a cross-research field with the main purpose of understanding the surrounding environment as closely as possible to human perception. The image processing systems is continuously growing and expanding into more complex systems, usually tailored to the certain needs or applications it may serve. To better serve this purpose, research on the architecture and design of such systems is also important. We present the End-to-End Computer Vision Framework, an open-source solution that aims to support researchers and teachers within the image processing vast field. The framework has incorporated Computer Vision features and Machine Learning models that researchers can use. In the continuous need to add new Computer Vision algorithms for a day-to-day research activity, our proposed framework has an advantage given by the configurable and scalar architecture. Even if the main focus of the framework is on the Computer Vision processing pipeline, the framework offers solutions to incorporate even more complex activities, such as training Machine Learning models. EECVF aims to become a useful tool for learning activities in the Computer Vision field, as it allows the learner and the teacher to handle only the topics at hand, and not the interconnection necessary for visual processing flow.


2014 ◽  
Vol 70 (6) ◽  
pp. 955-963 ◽  
Author(s):  
Ewa Liwarska-Bizukojc ◽  
Marcin Bizukojc ◽  
Olga Andrzejczak

Quantification of filamentous bacteria in activated sludge systems can be made by manual counting under a microscope or by the application of various automated image analysis procedures. The latter has been significantly developed in the last two decades. In this work a new method based upon automated image analysis techniques was elaborated and presented. It consisted of three stages: (a) Neisser staining, (b) grabbing of microscopic images, and (c) digital image processing and analysis. This automated image analysis procedure possessed the features of novelty. It simultaneously delivered data about aggregates and filaments in an individual calculation routine, which is seldom met in the procedures described in the literature so far. What is more important, the macroprogram performing image processing and calculation of morphological parameters was written in the same software which was used for grabbing of images. Previously published procedures required using two different types of software, one for image grabbing and another one for image processing and analysis. Application of this new procedure for the quantification of filamentous bacteria in the full-scale as well as laboratory activated sludge systems proved that it was simple, fast and delivered reliable results.


Author(s):  
Scott A. Raschke ◽  
Roman D. Hryciw ◽  
Gregory W. Donohoe

Laboratory experiments are typically performed on particulate media to study stress-deformation behavior and to verify or calibrate computer models from controlled or measured boundary stresses and displacements. However, such data do not permit the formation of shear bands, displacement fields within flowing granular media, and other small-scale localized deformation phenomena to be identified. Described are two semiautomated computer vision techniques for accurately determining the two-dimensional displacement field in granular soils from video images obtained through a transparent planar viewing window. The techniques described are applicable for studying the behavior of particulate media under plane strain and certain axisymmetric test conditions. Digital image processing and analysis routines are used in two different computer programs, Tracker and Tracer, Tracker uses a graphical user interface that allows individual particles to be selected and tracked through a sequence of digital video images. A contrast edge detection algorithm delineates the two-dimensional projected boundaries of particles. The location of the centroid of each particle selected for tracking is determined from the boundary to quantify the trajectory of each particle. Tracer maps the trace or trajectory of specially dyed fluorescent particles in a sequence of video frames. A thresholding technique segments individual particle trajectories. Together, Tracker and Tracer provide a set of tools for identifying small-scale displacement fields in particulate assemblies deforming under either quasi-static or rapid loading (such as gravity flow).


2010 ◽  
Vol 2010 (1) ◽  
Author(s):  
João Manuel R. S. Tavares ◽  
R. M. Natal Jorge

PLoS Biology ◽  
2018 ◽  
Vol 16 (3) ◽  
pp. e2003904 ◽  
Author(s):  
M. Flori Sassano ◽  
Eric S. Davis ◽  
James E. Keating ◽  
Bryan T. Zorn ◽  
Tavleen K. Kochar ◽  
...  

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