Center for Biomedical Image Computing & Analytics (CBICA)
CBICA focuses on the development and application of advanced computation techniques.
Philadelphia, PA
Pinned Repositories
BrainMaGe
Brain extraction in presence of abnormalities, using single and multiple MRI modalities
CaPTk
Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
CBICA_Toolkit
This is a toolkit with basic functionality to help C++ projects
CmdParser
An easy to use Command Line Parser and Common Workflow Language (CWL) specification creater/reader
Deep-LIBRA
DeepSeA
Automatic 3D whole breast segmentation in breast MRI
FigureGenerator
This helps creating high quality figures for use in manuscripts and presentations.
HistoReg
Framework for registration of sequential digitized histology slices
niCHART
The neuro-imaging brain aging chart [niCHART] is a comprehensive solution to analyze standard structural and functional brain MRI data across studies. [niCHART] and the associated pre-processing tools implement computational morphometry, functional signal analysis, quality control, statistical harmonization, data standardization, interactive visual
Tutorials
Here, we will be showcasing our seminar series “CPP for Image Processing and Machine Learning” including presentations and code examples. There are image processing and machine learning libraries out there which use C++ as a base and have become industry standards (ITK for medical imaging, OpenCV for computer vision and machine learning, Eigen for linear algebra, Shogun for machine learning). The documentation provided with these packages, though extensive, assume a certain level of experience with C++. Our tutorials are intended for those people who have basic understanding of medical image processing and machine learning but who are just starting to get their toes wet with C++ (and possibly have prior experience with Python or MATLAB). Here we will be focusing on how someone with a good theoretical background in image processing and machine learning can quickly prototype algorithms using CPP and extend them to create meaningful software packages.
Center for Biomedical Image Computing & Analytics (CBICA)'s Repositories
CBICA/CaPTk
Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
CBICA/BrainMaGe
Brain extraction in presence of abnormalities, using single and multiple MRI modalities
CBICA/niCHART
The neuro-imaging brain aging chart [niCHART] is a comprehensive solution to analyze standard structural and functional brain MRI data across studies. [niCHART] and the associated pre-processing tools implement computational morphometry, functional signal analysis, quality control, statistical harmonization, data standardization, interactive visual
CBICA/Deep-LIBRA
CBICA/FigureGenerator
This helps creating high quality figures for use in manuscripts and presentations.
CBICA/DeepMRSeg
CBICA/NiChart_Project
Neuro Imaging Chart of AI-based Imaging Biomarkers
CBICA/MRISnapshot
A QC tool for verification of datasets with MRI images and derived masks
CBICA/OPM
OpenSlide Patch Manager
CBICA/NiChart_Tissue_Segmentation
Brain tissue segmentation using FSL FAST and DLICV
CBICA/DeepMRSeg-Models
CBICA/GBMSurvival_2023
CBICA/MICO
CBICA/NiChart_Harmonize
Statistical harmonization package in NiChart
CBICA/NiChart_Viewer
Visualization tool for Neuroimaging Chart (NiChart) imaging descriptors and biomarkers
CBICA/MLSeminarSandbox
CBICA/TIP
Translational Imaging Pipelines
CBICA/BrainSegmenter
CBICA/BRIDGEPORT
Source for https://www.cbica.upenn.edu/bridgeport and documentation of the GWAS dataset
CBICA/cbica.github.io
CBICA/DLICV
A repository that allows users to apply the DLICV method to their brain imaging data.
CBICA/DLMUSE
A repository that allows users to apply the DLMUSE method to their brain imaging data.
CBICA/gandlf_experiments_template
CBICA/NiChart_DLMUSE
CBICA/NiChart_Website
The Landing page for the NiChart project
CBICA/NiChart_Workflows
CBICA/qt
UNCHANGED distribution of Qt_5.10.1 to satisfy license requirement
CBICA/RESPOND
CBICA/spare_score
Compute SPARE scores to detect characteristic feature patterns
CBICA/SurrealGAN