Code Ocean

United States of America

278 Works

Generalized 3D Fragmentation Index Derived From Lidar Point Clouds

Vaclav Petras
Point clouds with increased point densities create new opportunities for analyzing landscape structure in 3D space. Taking advantage of currently acquired dense point clouds we have extended a 2D forest fragmentation index developed for regional scale analyses into a 3D index for analyzing vegetation structure at a much finer scale. We applied this method to a point cloud obtained by airborne lidar capturing a suburban area with mixed forest cover. This is a modified version...

Data Visualization Code for: Quantitation of Cell Type-Specific Responses to Brassinosteroid by Deep Sequencing of Polysome-Associated Polyadenylated RNA

Elizabeth T Bartom
This R script takes a counts table to plot and a gene list (where the "genes" should be a unique subset of the row names in the table). It creates both a hierarchically clustered heatmap of the subset of the table indexed by the gene list, as well as a text based table of the same underlying data in the same row order.

CDBS: Modified Shape Signature for Concave Boundaries Description: Application to Skin Lesion Classification

Saeid Amouzad Mahdiraji
This code is prepared for the submitted paper Modified Shape Signature for Concave Boundaries Description: Application to Skin Lesion Classification in the journal of IEEE Journal of Biomedical and Health Informatics. In the paper, we propose a computer-aided diagnosis (CAD) system for detecting melanoma skin lesion. The aim of the paper is to develop a new shape descriptor to analyze the contour irregularity of shapes, which is called Convex Deficiency-Based Signature (CDBS). The main m_file...

Code for: Self-esteem, relationship threat, and dependency regulation: Independent replication of Murray, Rose, Bellavia, Holmes, and Kusche (2002) Study 3

Lorne Campbell
Across three studies, Murray, Rose, Bellavia, Holmes, and Kusche (2002) found that low self-esteem individuals responded in a negative manner compared to those high in self-esteem in the face of relationship threat, perceiving their partners and relationships less positively. This was the first empirical support for the hypothesized dynamics of a dependency regulation perspective, and has had a significant impact on the field of relationship science. In the present research, we sought to reproduce the...

A Standard for the Scholarly Citation of Archaeological Data

Ben Marwick
How do archaeologists share their research data, if at all? We review what data are, according to current influential definitions, and previous work on the benefits, costs and norms of data sharing in the sciences broadly. To understand data sharing in archaeology, we present the results of three pilot studies: requests for data by email; review of data availability in published articles, and analysis of archaeological datasets deposited in repositories. We find that archaeologists are...

FP-ANR: A representation format to handle floating-point cancellation at run-time

David Defour
Implementation of the FP-ANR format which handle floating-point cancellation at run time. When dealing with floating-point numbers there are several sources of error which can drastically reduce the numerical quality of computed results. Among those errors, one of the loss of significance or cancellation, which occurs during for example, the subtraction of two nearly equal numbers. In this article, we propose a representation format named Floating-Point Adaptive Noise Reduction FP-ANR. This format embeds cancellation information...

Features extraction based on Beta-Elliptic Model and Fuzzy Elementary Perceptual Codes

Thameur Dhieb
The presented code consists of the preprocessing and the segmentation of online handwriting into a sequence of Beta strokes in a first step. Then, from each Beta stroke, we extract a set of static and dynamic features using four features extraction techniques based on the Beta-Elliptic model and the Fuzzy Elementary Perceptual Codes. Next, all the segments which are composed of N consecutive Beta strokes are categorized into groups and subgroups according to their position...

Approximate Drop Volume from SEM Image

Atif Anwer
Objective: Approximate volume of drops in image taken under a Scanning Electron Microsocpe (SEM) The objective was to detect and approximate the volume of drops in a Pipette/Test Tube image, taken under a Scanning Electron Microsocpe (SEM). The source was a research problem for a PostGrad Student/friend in Chemical Engineering Department, UTP. The Matlab code does the following: Detects and idendifies drops in the SEM image Draws a boundary of the drops detected with centers...

Mapping the Universe of Registered Reports

Tom Hardwicke
Selection pressures for significant results may infuse bias into the research process. We evaluated the implementation of one innovation designed to mitigate this bias, ‘Registered Reports’, where study protocols are peer-reviewed and granted in-principle acceptance (IPA) for publication before the study has been conducted. As of February 2018, 91 journals had adopted Registered Reports and 91 Final Reports had been published. Psychology journals are the principal adopters, but expansion has begun into medicine, social science,...

A Computational Framework for Cortical Learning

Roland Suri
A Computational Framework for Cortical Learning Roland E. Suri*, Biological Cybernetics, https://doi.org/10.1007/s00422-004-0487-1 Recent physiological findings revealed that long-term adaptation of the synaptic strengths between cortical pyramidal neurons depends on the temporal order of presynaptic and postsynaptic spikes, which is called Temporally Asymmetric Hebbian (TAH) learning. Here I prove by analytical means that a physiologically plausible variant of TAH learning adapts synaptic strengths such that the presynaptic spikes predict the postsynaptic spikes. This hypothesis implies a...

TOP-DBS: Enhancement of Protein β-sheet Topology Prediction using Maximum Weight Disjoint Path Cover

Toktam Dehghani
Predicting β-sheet topology (β-topology) is one of the most critical intermediate steps towards protein structure and function prediction. The β-topology prediction problem is defined as the determination of the optimal arrangement of β-strand interactions within protein β-sheets. Significant efforts have been made to predict β-topologies. However, due to the inaccurate determination of interactions among β-strands and the huge topological space of proteins with a large number of β-strands, more efficient methods are required to improve...

Comparison of multi-hardware parallel implementations for a phase unwrapping algorithm

Francisco J. Hernandez-Lopez
Parallel implementation of a phase unwrapping algorithm named Accumulation of Residual Maps (ARM), for different parallel multicore architecture such as: CPU-multicore, Xeon Phi coprocessor and Nvidia GPU.

Semi-Laplacian-deep-network

Haikel Alhichri
This paper deals with the problem of the classification of large-scale very high resolution (VHR) remote sensing (RS) images and in a semi-supervised scenario where we have a limited training set. Typical pixel-based classification methods are unfeasible for large-scale VHR images, and so as a practical and efficient solution, we propose to subdivide the large image into a grid of tiles, and then classify the tiles instead. Our proposed method uses the power of a...

Intentional Aliasing Method to Improve Modulated Wideband Converter

Jehyuk Jang
A simulation MATLAB script is given to demonstrate AMWC, which has been proposed in our associated publication, "Intentional Aliasing Method to Improve Sub-Nyquist Sampling System". AMWC, aliased modulated wideband converter, improves modulated wideband converters (MWC) in terms of sub-Nyquist sampling performance per given hardware resources. MWC is a sub-Nyquist sampling system, which compresses the spectrum of an analogue wideband radio-frequency signal using pseudo-random signals (PRS). Once the wideband spectrum is well-compressed, conventional analog-to-digital converters (ADC)...

Label-Free Dynamic Segmentation and Morphological Analysis of Subcellular Optical Scatterers

Mohammad Naser
Abstract. Imaging without fluorescent protein labels or dyes presents significant advantages for studying living cells without confounding staining artifacts, and with minimal sample preparation. Here, we combine label-free Optical Scatter Imaging (OSI) with digital segmentation and processing to create dynamic subcellular masks, which highlight significantly scattering objects within the cells’ cytoplasms. The technique is tested by quantifying organelle morphology and redistribution during cell injury induced by calcium overload. Objects within the subcellular mask are first...

TOP-DBS: Enhancement of Protein β-sheet Topology Prediction using Maximum Weight Disjoint Path Cover

Toktam Dehghani
Top-DBS 1.0 Prediction of beta-strand pairs, beta-strand pairing direction, and beta-sheet topology Knowledge Engineering Research Group (KERG), Department of Computer Engineering, Faculty of Engineering, Ferdowsi University of Mashhad, Iran. Home page: https://kerg.um.ac.ir/ ; Email: kerg@um.ac.ir Contact: Toktam Dehghani Ph.D. Candidate and Researcher, Department of Computer Science and Software Engineering, Faculty of Engineering, Ferdowsi University of Mashhad, Iran. Dehgani.toktam@mail.um.ac.ir Copyright (C) 2018 Toktam Dehghani The program is free for scientific/academic use. The software must not be...

Parasitic Self and Mutual Inductances of Thin-Film Capacitors

Joaquin Bernal Mendez
Program for calculating parasitic self and mutual inductances of shunt-capacitor filters constructed with one, two or three thin-film capacitor placed in close proximity. Compares performances of several arrangements of thin film capacitors: 1) One capacitor 2) Two capacitors with currents in same direction (parallel) 3) Two capacitors with currents in opposite direction (anti-parallel) 4) Three capacitors with currents in same direction (parallel) 5) Three capacitors with currents in opposite direction (anti-parallel)

Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Pedro Coelho
This project contains the software used in the analyses presented in the paper "Similarity of the dog and human gut microbiomes in gene content and response to diet" by Luis Pedro Coelho, Jens Roat Kultima, Paul Igor Costea, Coralie Fournier, Yuanlong Pan, Gail Czarnecki-Maulden, Matthew Hayward, Sofia K. Forslund, Thomas Sebastian Benedikt Schmidt, Patrick Descombes, Janet R. Jackson, Qinghong Li, Peer Bork

A network-based conditional genetic association analysis of the human metabolome

Sodbo Sharapov
The repository stores all code and data necessary for reproducing the results of cGAS paper (doi:https://doi.org/10.1101/096982). The results of the paper were obtained from analysis of GWAS summary data (for more details see paper). "Data" folder stores GWAS summary data, SNP information file and correlation matrices. "Scripts" folder stores R functions for applying cGWAS to summary gwas data.

Competition EEG

Nicole Rafidi
Code for reproducing the main analysis of: Reductions in Retrieval Competition Predict the Benefit of Repeated Testing Nicole S. Rafidi, Justin C. Hulbert, Paula Pacheco, and Kenneth A. Norman Reproduces Figure 7 and with modifications can reproduce Figures S2-4

Competition EEG

Nicole Rafidi
Code for reproducing the main analysis of: Reductions in Retrieval Competition Predict the Benefit of Repeated Testing Nicole S. Rafidi, Justin C. Hulbert, Paula Pacheco, and Kenneth A. Norman Reproduces Figure 7 and with modifications can reproduce Figures S2-4

EMPOWER Pencil Beam

Thomas McIntyre
This capsule contains the Biomedical Optics Pencil Beam simulation using EMPOWER. I've added the Monte Carlo Results to the program so they may be better compared.

RTRMC - Low-rank matrix completion via preconditioned optimization on the Grassmann manifold

Nicolas Boumal
RTRMC is an algorithm to solve the low-rank matrix completion problem. This is notably useful in recommender systems (for example, to recommend movies to people based on movies they have rated in the past and based on the ratings obtained from other users as well.) The algorithm runs Manopt (a toolbox for optimization on Riemannian manifolds) on a non-convex formulation of the low-rank matrix completion problem on the Grassmann manifold.

EMPOWER Point Source

Thomas McIntyre
This capsule contains the Biomedical Optics Point Source simulation using EMPOWER. I've added the Monte Carlo Results to the program so they may be better compared.

Competition EEG

Nicole Rafidi
Code for reproducing the main analysis of: Reductions in Retrieval Competition Predict the Benefit of Repeated Testing Nicole S. Rafidi, Justin C. Hulbert, Paula Pacheco, and Kenneth A. Norman Reproduces Figure 7 and with modifications can reproduce Figures S2-4

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