Contributors: Massimo Salvi
... This repository contains the FAST algorithm graphical user interface and some sample image used in the following work: - Salvi M., Cerrato V., Buffo A., and Molinari F., "Automated Segmentation of Brain Cells for Clonal Analyses in Fluorescence Microscopy Images", J Neurosci Methods 2019 (DOI: 10.1016/j.jneumeth.2019.108348) ABSTRACT The understanding of how cell diversity within and across distinct brain regions is ontogenetically achieved is a pivotal topic in neuroscience. Clonal analyses based on multicolor cell labeling represent a powerful tool to tackle this issue and disclose lineage relationships, but produce enormous sets of fluorescence images, leading to time consuming analyses that may be biased by the operator’s subjectivity. Thus, time-efficient automated software are needed to analyze images easily, accurately and without subjective bias. In this paper, we present a fully automated method, named FAST (‘Fluorescent cell Analysis Segmentation Tool’), for the segmentation of neural cells labeled by multicolor combinations of fluorophores and for their classification into clones. The proposed method was tested on 77 high-magnification fluorescence images of adult mouse cerebellar tissues acquired using a confocal microscope. Automatic results were compared with manual annotations and two open-source software designed for cell detection in microscopic imaging. The algorithm showed very good performance in the cellular detection and in the assignment of the clonal identity. To the best of our knowledge, FAST is the first fully automated technique for the analysis of cellular clones based on combinatorial expression of fluorescent proteins. The proposed approach allows to perform clonal analyses easily, accurately and objectively, overcoming those biases and errors that may result from manual annotations. Moreover, it can be broadly applied to the quantification and colocalization within cells of fluorescent markers, therefore representing a versatile and powerful tool for automated quantitative analyses in fluorescence microscopy.
Contributors: Anders Thomsen, Morten Kristiansen, Ewa Kristiansen, Benny Endelt
... The data describes the measurement of a v-bend shape formed during multi-scan laser forming. The purpose of the measurements was to determine the dynamic response during laser forming of a v-bend. A measurement scanner was used to measure the height of a line perpendicular to the heating scan line of a laser during laser forming. In order to estimate a surface, 105 samples were made with identical settings with the measurement scanner moved along the heating scan line between samples. A total of 21 positions along the heating scan line were measured. Each position was measured using 5 samples. Due to a memory problem, the measurement scanner could only measure about 3.12 seconds at a time. The measurement scanner is started slightly before each heating scan line starts. Furthermore, each heating scan line is split into its own text file in the data set. This data set contains 21 folders, one for each position of the measurement scanner along the heating scan line. The folders are named as 'ymm', where y is the distance from the trailing edge of the heating scan line, '_' is used instead of decimals here. Each folder contains 30 text files, 6 for each of the samples used, structured as (x, y, z, t). Each file is named as 'sample_i_plate_j_scannumber_k.txt', where i is the sample number (1-5) at this position, j is the plate number (1 or 2), k is the scan number (1-6). Scan number 6 does not contain any heating, but is set as a final measurement of about 60 seconds after forming. Warning: The unzipped data fill 51.6 GB
Data/Software for "Presynaptic Mitochondria Volumes and Complexity of Subsynaptic Distribution Increase During Development at a High-fidelity Synapse"
Contributors: Connon I. Thomas, Christian Keine, Satoko Okayama, Rachel Satterfield, Morgan Musgrove, Debbie Guerrero-Given, Naomi Kamasawa, Samuel M. Young, Jr.
... Contains data and software from the publication: "Presynaptic Mitochondria Volumes and Complexity of Subsynaptic Distribution Increase During Development at a High-fidelity Synapse" currently under review. The preprint to this data set has been published on bioRxiv (https://doi.org/10.1101/689653). In this study, we created a helper-dependent adenoviral vector (HdAd) to co-express cytoplasmic EGFP and a genetically encoded peroxidase marker (mito-APEX2) at the calyx of Held, an excellent model for deciphering regulatory mechanisms of presynaptic function. ABSTRACT: The calyx of Held, a large glutamatergic presynaptic terminal in the auditory brainstem undergoes developmental changes to support the high action-potential firing rates required for auditory information encoding. In addition, calyx terminals are morphologically diverse which impacts vesicle release properties and synaptic plasticity. Mitochondria influence synaptic plasticity through calcium buffering and are crucial for providing the energy required for synaptic transmission. Therefore, it has been postulated that mitochondrial levels increase during development and contribute to the morphological-functional diversity in the mature calyx. However, the developmental profile of mitochondrial volumes and subsynaptic distribution at the calyx of Held remains unclear. To provide insight on this, we developed a helper-dependent adenoviral vector (HdAd) that expresses the genetically encoded peroxidase marker for mitochondria, mito-APEX, at the mouse calyx of Held. We developed protocols to detect labeled mitochondria for use serial block face SEM (SBF-SEM) to carry out semi-automated segmentation of mitochondria, high-throughput whole terminal reconstruction and presynaptic ultrastructure in mice of either sex. Subsequently, we measured mitochondrial volumes and subsynaptic distributions at the immature postnatal day 7 (P7) and the mature (P21) calyx. We found an increase of mitochondria volumes in terminals and axons from P7 to P21 but did not observe differences between stalk and swelling subcompartments in the mature calyx. Based on these findings, we propose that mitochondrial volumes developmentally increase to support high firing rates but have limited contribution to morphological-functional diversity at the calyx. Data are sorted by the figures they appear in. Media (movies and 3D models) and custom-written software are located in separate folders.
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Contributors: Liam Brown
... 9.1 Video: Contains an edited video of the NIVALIS I prototype robot navigating in horizontal and vertical 150 mm pipes and navigating through an elbow with manual control. 9.2 Video: Contains an edited video of the FURO I prototype robot navigating through an elbow with manual control. 9.3 Video: Contains an edited video of the FURO II prototype robot navigating through an elbow with the autonomous elbow controller running. CAD 9.1: Solidworks files for the design of the FURO II prototype
Contributors: Carlos Palacio
... Raw data for the internal Project 2016210 "Preparation and characterization of magnetic nanoparticles based in ferrites"--> UAN-UdeA.
Contributors: Jan Sedlak
... The presented software for analysis of muscle coordination obtained during periodic movement is based on multi-channel surface EMG processing. Output data of software includes analysis of averaged SEMG profiles and muscle activity timing. The algorithm is available as MATLAB standalone executable application with free access. Attachment of zip file contain demo SEMG data of gait, running and rowing. Input data are imported into software in MAT-file or Comma-separated values format with a structure described in the attached user manual. This software could help to make multichannel SEMG analysis more time-effectively.
Contributors: Prashant K. Jha, Robert Lipton
... We share the data used in publishing the article "Numerical convergence of finite difference approximations for state based peridynamic fracture models", see https://doi.org/10.1016/j.cma.2019.03.024. The data set comprises of raw data produced by computational code, post-processed files, and python script files. We consider finite difference approximation of a nonlinear state-based peridynamic model. We run simulation for two problems. In the first problem, we have a square domain with verticle pre-crack originating from the middle of the bottom edge. We apply a constant velocity boundary condition along the horizontal axis on the bottom layer. In response to the boundary conditions, the crack propagates vertically. The data correspond to three different horizons, 2mm, 4mm, and 8mm. For each horizon, we have three results, each corresponding to mesh size horizon/2, horizon/4, and horizon/8. From the approximate displacement fields, we compute the rate of convergence with respect to mesh size, for each fixed horizon. These are post-processed data and can be found in "postprocessing" folder of Example 1. In the second problem, we consider a rectangle domain which is supported at two regions (left and right) near the bottom edge. On the portion of the top edge, we apply a monotonically increasing in time force in the downward direction. We run simulation when the sample has just one vertical pre-crack originating from the middle of the bottom edge and when the sample has two vertical pre-cracks symmetrically located and originating from the bottom edge. We plot the damage at multiple times and show that the crack propagates upwards in response to applied load. All computations are carried out using an in-house developed code. In this data set, we have not shared the computational code. However, we plan on making the code public in the future. If you are interested in our code and if you have some collaborative ideas please feel free to get in touch.
Contributors: Qing Zhu, Ling Ding, Zhenguo Zi, SHUJUN GAO, Chong Wang, Yuyan Wang, Caixia Zhu, Zhenghong Yuan, Fang Wei, Qiliang Cai
... Aurora B (AURKB) kinase, a central regulator of chromosome segregation and cytokinesis, is aberrantly expressed in various cancer cells. However, the relationship of AURKB and oncogenic viruses in cancer progression remains unclear. Here, we reveal that N-cleaved isoforms of AURKB exist in several oncovirus-associated tumor cells and patient cancer tissues, including Kaposi’s sarcoma herpesvirus (KSHV), Epstein-Barr virus (EBV), and human papillomavirus virus (HPV). Mechanistically, in KSHV-infected tumor cells，the latent viral antigen LANA cleaves AURKB Asp76 in a serine protease-dependent manner. The N’-cleaved AURKB relocalizes to the spindle pole and promotes the metaphase-to-telophase transition in mitotic cells. Introduction of N’-AURKB but not C’-AURKB promotes colony formation and malignant growth of tumor cells in vitro and in vivo using a murine xenograft model. Altogether, our findings uncover a proteolytic cleavage mechanism by which oncoviruses induce cancer cell segregation and tumorigenesis.
Dataset for the Paper MEdit4CEP-CPN: An Approach for Complex Event Processing Modeling by Prioritized Colored Petri Nets
Contributors: Juan Boubeta-Puig, Gregorio Diaz, HERMENEGILDA MACIA, Valentin Valero, Guadalupe Ortiz
... These files should be considered as additional material for the paper "MEdit4CEP-CPN: An Approach for Complex Event Processing Modeling by Prioritized Colored Petri Nets". Its aim is to show how our MEdit4CEP-CPN approach works.
Contributors: SARV PRIYA, Simon Ching-Shun Kao
... Real time fluoroscopy shows the malaligned/fractured distal tip of the longer catheter that appears to be still attached with no large flip-flop movement.