Search Results for "tissue"
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Showing 53 open source projects for "tissue"
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FortiGate-VM delivers comprehensive security and scalable VPN connectivity for your AWS workloads, while native AWS integrations unlock broad coverage for your environment. Now with support for AWS Graviton2 instances, FortiGate lets you optimize price performance and reduce your Amazon EC2 costs by up to 20 percent. Deploy today in AWS Marketplace.
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Deploy Red Hat Ansible Automation Platform on Microsoft Azure for a strategic automation solution that allows you to orchestrate, govern and operationalize your Azure environment.
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CliMA Land
Everything within the Land model
CliMA Land is a next generation Land Surface Model (LSM) designed to use the broadly available remote sensing data as well as ground-based flux measurements. CliMA Land is a highly modular platform to promote research at different scales from tissue to organ, whole plant, and ecosystem. Therefore, we deliver CliMA Land via a patch of packages (also referred to as sub-modules) to reduce the time used to initialize a research project. As a result, the repository is more a collection of tutorials... -
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FibroSoft
Histology staining analysis and quantification tool.
A histology staining analysis and quantification tool based on machine learning. -
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Cell Migration Assay
Cell migration is regulated by the relevant signaling molecules.
Cell migration is a fundamental process that involves the translation of cells from one location to another by adopting different motility modes, such as mesenchymal, amoeboid, or collective migration. Cell migration is essential for the development and maintenance of multicellular organisms. It also plays a key role in cell migration-mediated tissue organization, organogenesis, and homeostasis, especially in the immune response and cancer spreading which are the hotspots of clinical studies... -
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Cell proliferation is defined as the process that leads to an increase in the number of cells and the balance between cell divisions and cell loss. Cell proliferation plays an important role in regular tissue and cellular homeostasis for proper growth, development and maintenance of the organism. Moreover, abnormal cell proliferation is associated with different diseases, such as cancer. The cell proliferation assays can be used for pharmaceutical drug discovery and diagnostic purposes.
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Collaborate is customizable case management software for non-profits and social services agencies with teams of 5+ staff.
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deps.cloud
Index and query dependencies across your company's private repository
... organization manages their repositories and dependencies. Do you use a monorepo or do you have a repo per service? Is each service allowed their own set of dependencies or do you pull from one common pool? Dependencies are the connective tissue of deps.cloud. A dependency defines a relationship between two modules. Specifically a directed, versioned, and historical relationship. It’s this type of relationship that makes modeling data in traditional data stores difficult. -
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Geroes is a deep learning-based system dedicated to evaluating gene contribution in defining tissue specificity.
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PBTK Optimizer
Application for optimization of parameters in PBTK models
Physiologically based toxicokinetic (PBTK) modeling offers great promise in environmental risk assessment, potentially speeding up dose-response studies while minimizing animal testing. Some limitations exist in the PBTK field, such as difficulty of model development and a lack of application specific software tools to help modelers. Some parameters used in PBTK models, such as tissue weights, are easily measure. Other parameters can be determined through in-vitro experiments or through... -
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PMCGPU
Parallel simulators for Membrane Computing on the GPU
Membrane Computing is a new research area (within Natural Computing) that aims to provide computing devices abstracted from the functioning and structure of living cells. These devices are called P systems. The objective of this project (PMCGPU) is to bring together all the researchers working on the development of parallel simulators for P systems, specially those using the GPU (e.g. CUDA, OpenCL, etc). Other parallel platforms are also welcome (multicore and manycore, FPGAs,... -
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Tissue Simulation Toolkit is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.
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Our robust pre-built connectors and our no-code, drag-and-drop interface makes it easy and fast to automatically sync vendors, invoices, and invoice payment data between Tipalti and your ERP or accounting software.
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OncoBase
A platform for decoding regulatory somatic mutations in human cancers
Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers. The vast majority of identified somatic mutations are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput chromosome conformation capture (3C)-based technologies, genome-scale long-range chromatin interactions were detected, and distal target genes of regulatory elements... -
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Snapshot Demo
Snapshot models the genes and reactions within human cells
Snapshot is a poly-omics model of the human cell allowing you to edit genes and see how it affects cell functionality and what diseases might arise. The full Genome scale metabolic model consists of the following: 92 Genes 53 Reactions 109 Metabolites 3 Cellular Compartments 7 Diseases Which can be found here for only £2!: https://www.scarboroughbiotech.com/ Note demo version is a much smaller genome scale model. -
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FATCALC-ImageJ is an ImageJ macro (fully automated) for unsupervised fat segmentation in magnetic resonance imaging. It was developed for GE T1 2-points Dixon sequences (fat only image). FATCALC independently evaluates the volumes of visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT).
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ImagingAnalysis
Direct tissue-level image quantification package for Mathematica
ImagingAnalysis is a Mathematica package that performs grid-based analysis of time-lapse imaging data saved in a sequence of TIFF files. This package requires Mathematica 7.0. Revised on 14 May 2017: Bugs are fixed and incompatibility issues are resolved. The current version runs on Mathematica 11. -
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3DimViewer
3DimViewer is a lightweight 3D viewer of medical DICOM datasets.
3DimViewer is a lightweight 3D viewer of medical DICOM datasets that is distributed as open source software. The viewer is multiplatform software written in C++ that runs on Windows, Mac OS X and Linux systems. 3DimViewer source codes are available on Bitbucket (https://bitbucket.org/3dimlab/3dimviewer). Video tutorials can be found on YouTube (https://www.youtube.com/playlist?list=PLCvwUmKRw9ZO4YexLKEXmw_2jPo-kXVRn). -
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Tissue Microbiota
The characterization of novel tissue microbiota
Scripts to generate the 466 MiSeq indexes and 16S metagenomics figures to characterize the microbiota in mock communities and the following tissues: Ileum, Feces, MAT, Liver, Brain, Heart, Muscle. -
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MRiLab
A Numerical MRI Simulation Platform
... technique. The main MRiLab simulation platform combined with those toolboxes can be applied to customize various virtual MR experiments which can serve as a prior stage for prototyping and testing new MR technique and application. If you find MRiLab useful for your work, please cite this paper: Fast Realistic MRI Simulations Based on Generalized Multi-Pool Exchange Tissue Model. IEEE Transactions on Medical Imaging. 2016. doi: 10.1109/TMI.2016.2620961 -
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experix laboratory control system
instrument control, data acquisition display and analysis
... pipes. Interfaces accessible via commands and scripts: file i/o modelled on stdio and stdlib; usb control and bulk transfers; socket operations; webcam; graphics via framebuffer. Applications (not all available yet for download) include: cell poker (like an atomic force microscope); tissue mechanical tester; fluorescence photobleaching; alternating laser excitation fluorescence; fluorescence intensity distribution analysis; iverilog simulation analysis. -
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DuMuX
Porous-Media Simulator
... storage scenarios, environmental remediation problems, transport of therapeutic agents through biological tissue, and subsurface-atmosphere coupling. DuMuX is part of the OPM (Open Porous Media) initiative, opm-project.org. -
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O2 pathway and ROS generation model
Multi-scale Modeling of Skeletal Muscle ROS Generation
The production of reactive oxygen species (ROS) from the inner mitochondrial membrane is one of many fundamental processes governing the balance between health and disease. It is well known that ROS are necessary signaling molecules in gene expression, yet when expressed at high levels, ROS may cause oxidative stress and cell damage. Both hypoxia and hyperoxia may alter ROS production by changing mitochondrial PO2 (PmO2). This graphical user interface facilitates to parameterize and simulate... -
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reg_stack
For registering stacks of 2D images.
reg_stack is an extension to the open source project, NiftyReg, for the coregistration of a series of 2D images representing a 3D block tissue subjected to histological serial sectioning. The software performs a series of nonlinear image transformations across a kernel of user-specified size to restore data continuity, as the sectioning process results in misalignments and distortions. The NiftyReg package also includes optimizations for parallelization on either the CPU or GPU... -
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endo-MCML
MC model of Endoscopic Optical Spectroscopy for tubular organ
We present a Monte Carlo static light migration model (Endo-MCML) to simulate endoscopic optical spectroscopy for tubular organs such as esophagus and colon or organs lying behind tubular organs like prostate. Differ from the well-known multi-layered slab tissue model (MCML), our model employs multi-layered hollow cylinder which emitting and receiving light both from the inner boundary to meet the conditions of endoscopy. Inhomogeneous sphere can also be added in tissue layers to model cancer... -
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BoneSlicer
Experimental G-Code-Generator for variable density infill in FFF parts
BoneSlicer is an experimental G-Code-Generator written in Java that allows creating load-adapted infill for 3D printed (FFF) parts, inspired by the adaptive structures of trabecular bone tissue. It uses a simple structural Finite Element Analysis to determine the distribution of mechanical stress within the part and offers tools to generate an infill structure consisting of multiple subareas of varying infill density. Subdivision of the infill area can be based on a broad spectrum of FEA result... -
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ntcpcalc.py
python based ntcp calculation (LKB model, relative seriality model)
- command line python script that calculates the NTCP (Normal Tissue Complication Probability) # if parameters feed to the script directly run script as: # ./ntcpcalc.py 0 1 "dvh.txt" "Heart" shell # and via single questions to the user: # ./ntcpcalc.py userinp output would be as follows: NTCP=1.3% finished: - currently a number of different LKB (Lyman-Kutcher-Burman) model parameters and relative seriality models implemented - reads in differential DVH (dose-volume-histogram... -
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IHC Profiler
A plugin for the quantitative analysis of Immunohistochemistry samples
...-x- Full Publication and Citation: Varghese F, Bukhari AB, Malhotra R, De A (2014) IHC Profiler: An Open Source Plugin for the Quantitative Evaluation and Automated Scoring of Immunohistochemistry Images of Human Tissue Samples. PLoS ONE 9(5): e96801. doi:10.1371/journal.pone.0096801 Link: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0096801 -x-x-x-x-x-x-x- Your feedback would be highly appreciated. Please rate so we can work on improving it further. Thank you! -
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MMAD
Microarray Microdissection with Analysis of Differences (MMAD)
We have developed a new computational tool called MMAD, which is capable of performing robust tissue micro-dissection in silico, and which can improve the detection of differentially expressed genes. MMAD software is implemented in MATLAB. The MMAD.zip file contains a brief user guide and MATLAB source code for implementation of MMAD. Developers: David A Liebner, MD Kun Huang, PhD Jeffrey D Parvin, MD, PhD