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HIFIS Software Spotlights

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13-24 of 153

BrainPrint

Our BrainPrint tools provide shape descriptors of neuroanatomical structures and require a FreeSurfer or FastSurfer segmentation as a pre-processing step. BrainPrint is based on “ShapeDNA” a spectral shape descriptor.

Data analysis
MRI
open source
+ 1

Python

113

calibr8

calibr8 is a Python toolbox for likelihood-based calibration modeling and Bayesian inference. It supports uni- and multivariate problems, continuous & discrete distributions and includes ready to use models for many non-linear problems. It integrates with PyMC for advanced Bayesian inference.

Calibration
Data analysis
Earth & Environment
+ 4

Jupyter Notebook
Python

CellDetection

An open-source Python package, offering advanced AI methods for the identification and segmentation of biomedical objects, such as cells, in image data. Includes trained models that work out-of-the-box for a wide range of use cases.

cell counting
cell detection
cell segmentation
+ 9

Python
Dockerfile

Citation File Format

The Citation File Format (CFF) project provides a format and schema for plain text CITATION.cff files with human- and machine-readable citation information for software (and datasets). Developers/RSEs can include them in their repositories to let others know how to correctly cite their software.

Citation File Format
Information
metadata
+ 2

Python

CICMoD - A Climate Index Collection based on Model Data

The software provides a consistent and comprehensive collection of climate indices typically used to describe Earth System dynamics and serves as a new benchmark data set. It allows users to develop new machine learning methods and to compare their results to existing methods in an objective way.

Earth & Environment
FAIR Data
Image processing
+ 1

Jupyter Notebook
Python
Shell
+ 1

COMANDO

COMANDO is a next generation modeling framework for Component-Oriented Modeling and optimizAtion for Nonlinear Design and Operation of integrated energy systems.

Energy
ESD
ESD - Topic 2

Python

Copy-Paste Imputation (CPI) for Energy Time Series

This project provides a Python implementation of an imputation method for energy time series. The CPI method copies data blocks with similar characteristics and pastes them into gaps of the time series while preserving the total energy of each gap.

Earth & Environment
Energy
ESD
+ 2

Python

CrystFEL

CrystFEL is a suite of programs to process data from "serial crystallography" experiments.

crystallography
Matter
structural biology
+ 2

C
Julia
Python
+ 2

305

DataLad

DataLad is a tool for the joint management of code, data, and their relationship, built on top of the version control systems Git & git-annex. It adapts principles of open-source software development & distribution to address challenges of data management, data sharing, & digital provenance capture.

DataLad
data managment
data sharing
+ 8

Python
Shell
Makefile
+ 4

172

DataLad Container extension

This DataLad extension package equips DataLad's run/rerun functionality with the ability to transparently execute commands in containerized computational environments. On re-run, DataLad will automatically obtain any required container at the correct version prior execution.

DataLad
data managment
Workflow Execution

Python
Shell
Makefile
+ 2

DataLad NEXT extension

This DataLad extension is a staging area for add-ons, for performance upgrades, and user experience improvements. Unlike other topical extensions, the focus is on functionality with broad applicability.

data distribution
DataLad
data management

Python
Shell
Batchfile
+ 2

dCache

dCache is a system for storing and retrieving huge amounts of scientific data, distributed among a large number of heterogeneous server nodes, under a single virtual filesystem tree with a variety of standard access methods including NFSv4.1 (pNFS), FTP, WebDav and xroot.

data managment
FAIR Data

Java
JavaScript
XSLT
+ 14