Awesome Child Mind Institute — Research Teams Projects

A curated list of 83 active, non-fork public repositories from the Child Mind Institute — Research Teams organization.

This list is automatically generated using OpenAI GPT for description and categorization. Archived repositories and forks are excluded.

Table of Contents

• Data Processing (64)
• GitHub Tools (8)
• Neuroimaging Utilities (25)
• Python Libraries (60)
• Rust Projects (5)
• Sleep Data Analysis (3)
• Visualization Tools (16)
• Web Applications (17)

Data Processing

Repository	Language	Description
bids2table		bids2table is a Python tool that efficiently indexes BIDS datasets, allowing users to quickly search and index datasets locally or in the cloud, with support for S3 storage.
wristpy		wristpy is a Python package designed for processing and analyzing wrist-worn accelerometer data. It offers tools for loading sensor information, calibrating raw accelerometer data, calculating physical activity metrics, detecting non-wear and sleep periods, and accessing additional sensor data recorded by the watch.
helios-render-kaggle		This repository, helios-render-kaggle, provides a tool for visualizing sensor data from the Helios device, specifically tailored for the CMI - Detect Behavior with Sensor Data competition on Kaggle. It allows users to render sequences from the dataset based on specified filters and generate video files for analysis.
headjack		headjack is an interactive NIfTI image viewer designed for the terminal, offering seamless compatibility with various platforms like remote clusters and containerized environments, making it a valuable tool for researchers and developers.
nifti-stream		nifti-stream is a streaming parser for NIFTI-1 and NIFTI-2 neuroimaging files, optimized for client-side processing and progressive loading in web applications.
niftyone		NiftyOne is a platform for bulk visualization of large-scale neuroimaging datasets, utilizing FiftyOne features with popular neuroimaging Python packages.
cmi-docx		cmi-docx is a Python library that enhances the functionality of python-docx for working with .docx files. It offers features like find and replace, inserting paragraphs, and manipulating styles and formatting within documents.
MoBI-View		MoBI-View is a Python GUI application that provides real-time visualization of biosignal data from Lab Streaming Layer (LSL) streams, enabling researchers and clinicians to monitor and analyze various biosignals like EEG and physiological measurements through an intuitive interface.
C-PAC_slurm_testing		This repository enables C-PAC developers to run full regression tests on Bridges-2 cluster using SLURM job submission scripts.
quick-viz		This repository, "quick-viz," provides short and simple Python visualization scripts to easily generate visualizations for various types of data, such as TSV-stored matrices, Nii-stored 3D brain data, and surface mesh data. The tools are designed to streamline development and testing cycles by offering quick and easy-to-use utilities.
neurothumb		neurothumb is a Rust-based repository that serves as a neuroimaging file thumbnail generator and integration tool.
tsconcat		This repository provides a BIDS App and Python library for concatenating MRI time series, allowing users to combine BOLD time series from multiple datasets, sessions, subjects, or runs into a single file.
cross-species-mapper		This repository provides a webapp for translational exploration between humans and macaques, utilizing a Svelte frontend and a Python FastAPI backend.
actisleep-tracker		ActiSleep Tracker is a web application designed for annotating sleep data obtained from actigraphy data processed with the GGIR package. Users can visualize and annotate sleep periods using this tool.
actfast		actfast is a fast actigraphy data reader for Python, implemented in Rust. It supports reading data from Actigraph GT3X and GENEActiv devices, with planned support for Axivity CWA format.
hbn-ddp		This repository provides a Python preprocessing package, hbn-ddp, designed for handling the Healthy Brain Network clinician consensus diagnostic data. It transforms the data into a more organized format for analysis, allowing filtering by diagnostic certainty or time of diagnosis and creating visualizations of the diagnostic data.
yaspy		yaspy is a Python library for creating neuroimaging surface plots, ranging from simple screenshots to complex montages and publication-ready figures. It leverages PyVista, Matplotlib, and Pillow for its functionality.
nifti		This repository provides a lightweight NIfTI file reader and writer in C++, utilizing modern zlib for efficient operations.
gen192		gen192 is a Python-based 192 C-PAC pipeline generator that offers various pipelines, pipeline steps, connectivity measures, and nuisance regression options for neuroimaging analysis.
unifti		The "unifti" repository provides minimal header-only NIfTI definitions and utilities in C, capturing NIfTI 1.1 and 2 standard and extension codes, with features like portability, zero heap allocations, and utility functions for NIfTI file handling tasks.
ctk-functions		This repository contains Azure Functions written in Python for the Clinician Toolkit, offering services such as document conversion, intake form processing, grammatical correction, and text generation through a FastAPI backend.
loris-docker		This repository provides Docker builds for Loris, offering different container images with varying dependencies such as Loris, Loris-MRI, and MINC Toolkit, along with instructions for building and configuring the containers efficiently.
mobi-motion-tracking		mobi-motion-tracking is a Python package designed for processing and analyzing 3D motion tracking data. It offers tools to compare skeletal data against a gold standard, calculate similarity metrics like DTW, and generate labeled output files for further analysis.
MOBI_QC		MOBI_QC is a Python quality control pipeline tailored for assessing multimodal datasets, including EEG, Eye-tracking, Physiological signals, Audio, and Video data. It automates preprocessing, computes detailed quality control metrics for each modality, and generates PDF reports for easy review and documentation.
graphomotor		graphomotor is a Python toolkit designed for analyzing graphomotor data collected via Curious, offering feature extraction and visualization capabilities for tasks like spiral drawing, trails making, alphabetic writing, digit symbol substitution, and the Rey-Osterrieth Complex Figure Test.
noctsleepy		noctsleepy is a Python package that computes comprehensive sleep metrics from processed actigraphy data, allowing users to analyze sleep duration, efficiency, wake after sleep onset, and more within customizable nocturnal windows while handling daylight saving time transitions.
synthdata		This repository serves as a sandbox for generating and evaluating synthetic data using Python. It includes tools for data generation, evaluation, and parsing hierarchical structures from markdown documents.
headhunter		headhunter is a Python parser that extracts headings and hierarchical structures from Markdown files, supporting various heading formats, fuzzy matching, batch processing, and export to different formats.
elbow		Elbow is a lightweight Python library designed to transform specialized data into common tabular formats for analytics, offering scalability and ease of use. It allows users to extract diverse data into formats like Parquet for downstream analysis.
vmi-train		This repository provides a generic configurable mobile task designed to track objects using ShaderLab.
flowdump		flowdump is a NiPype workflow serializer designed for use with flowview, allowing users to execute workflows and save pre- and post-execution data to JSON files with ease.
BrainParsers		BrainParsers provides Kaitai struct grammars for parsing various brain imaging data formats.
cpac-log-muncher		This repository provides a Python tool, clmunch, for aggregating and summarizing logs generated by the C-PAC pipeline.
NeuRosetta		NeuRosetta provides GPT-4 translations of common operations in various brain imaging frameworks, aiming to facilitate researchers in switching between and learning different frameworks effortlessly.
survey_subsampling		This repository provides a package for reducing the size of complex survey instruments by identifying and retaining only the most predictive assessment items. It offers a data-driven approach to subsampling surveys like the CBCL based on their ability to predict diagnostic status.
bridges-cheatsheet		This repository provides a cheat sheet for efficiently using the Bridges2 compute cluster, including environment variable settings, useful commands for job management, Singularity/Apptainer configurations, Anaconda setup, C-PAC job file templates, and various utilities for enhancing workflow efficiency.
C-PAC_pre-commit_examples		This repository provides examples of using pre-commit in C-PAC for linting code and making changes in different branches.
ctk-markdown-to-sql		This repository provides a Rust tool for converting hierarchical markdown documents into SQL insertion queries. It parses markdown files into a tree structure and generates SQL commands to insert the parsed data into a database.
mindlogger-graphomotor-data		This repository parses MindLogger exports in Python using the Bidsi library.
bidsi		Bidsi is a Python library designed to assist in converting various data sources to BIDS format by providing classes and utilities for building and writing BIDS structured data.
multiecho-processing		This repository contains a Multiecho Preprocessing Pipeline project for processing multiecho fMRI data on C-PAC, providing steps for installation and usage.
cmi-ffmpeg-server		This repository likely contains a server application written in Rust that utilizes the FFmpeg multimedia framework for various media processing tasks.
MoBI_Docs		MoBI_Docs is a repository containing materials for the Child Mind Institute's Multimodal Brain/Body Imaging (MoBI) Core, focusing on standardizing research methods and developing software pipelines for data analysis and quality control.
doc-bot		The "doc-bot" repository contains the software architecture and cloud deployment details for a chatbot system involving Open WebUI, LiteLLM, and a custom proxy server, with Azure and AWS integrations for storage and processing.
resource-inventory		This repository is a web application that helps users search for resources used in the C-PAC software. It offers a user-friendly interface to browse and search through a comprehensive inventory of resources, with features like search functionality, dark mode, and direct links to specific lines in the GitHub repository.
hbn_correction		This repository provides a Python package for correcting data from the Healthy Brain Network dataset. It offers functionality to perform data corrections and includes a notebook example for reference.
tinyfeast		The "tinyfeast" repository is a Python project with no README file available.
graphomotor_cmi		This repository contains scripts to run the Graphomotor Protocol at the Child Mind Institute during the Summer of 2025. The main script, "graphomotor_full.py," encompasses the entire protocol.
tiny-mirror		This repository, tiny-mirror, provides functionality for generating concerning summaries using Python. It includes methods to obtain both final results and intermediate results for analyzing text entries.
awesome-childmindresearch		This repository is a curated list of 77 active, non-fork public repositories from the Child Mind Institute — Research Teams organization, generated using OpenAI GPT for description and categorization.
MoBI-AV		MoBI-AV is a Python application for recording audio and video simultaneously, offering device selection and synchronization capabilities, including integration with Lab Streaming Layer (LSL) for time-synchronizing recordings with other experimental data sources.
parent-tech-survey		This repository performs text analysis for the PPTOB Study.
zed2i_3d_capture		This repository provides the necessary Python code to record 3D motion tracking data from the ZED 2i stereo camera, enabling real-time body tracking and data collection with or without a live stimulus.
not-as-many-pipelines		This repository provides a diff checker tool for comparing original gen192 configurations with updated ones.
zed2i_3d_lsl_capture		This repository records 3D motion tracking data from the ZED 2i stereo camera and streams live markers to Lab Streaming Layer, saving the data in a format compatible with the mobi_motion_tracking package.
zed2i_motion_classifier		This Python repository, zed2i_motion_classifier, is designed for real-time movement classification using the ZED 2i stereo camera and streams frame-by-frame classifications over LSL (Lab Streaming Layer). It performs action, behavior, and position classification on a single person, streaming these classifications over LSL, and recording video to a .svo2 file.
MoBI-Markers		A Python GUI application for sending LSL (Lab Streaming Layer) markers used in neuroscience research, featuring a clean interface, real-time marker sending, status logging, and cross-platform compatibility.
MoBI-Neon-GUI		MoBI-Neon-GUI is a Python GUI application for recording video from Pupil Labs Neon devices with synchronized LSL markers, offering real-time video preview, recording controls, configurable save directory, and customizable output filenames with timestamp support.
MoBI-Physio-API		A Python API for PLUX biosignals devices with automatic sensor detection and Lab Streaming Layer (LSL) integration, supporting cross-platform usage and real-time data streaming.
helios_eval		This repository provides a tool for evaluating the results of the Helios Kaggle competition using Python.
neuromaps-prime		The neuromaps-prime repository provides a toolbox for integrating multiscale, multimodal annotations across non-human primate (NHP) brains, facilitating comprehensive comparative brain organization analyses. It extends the neuromaps ecosystem to offer unified access to various NHP brain datasets and specialized tools for NHP-specific analyses.
ctk-terraform		This repository manages Azure infrastructure for the CTK project using Terraform, organizing it into shared, development, and production environments with a focus on deploying the shared infrastructure first before environment-specific resources.
MoBI-Curious-LSL-Relay		This repository, MoBI-Curious-LSL-Relay, is a Python script that serves as an LSL Relay for the Curious app in the context of MoBI. It simplifies the setup process by handling dependencies automatically without the need for manual virtual environment creation or separate package installations.
anonymize-pii		This Python repository provides a text-based PII anonymizer tool that flags and anonymizes sensitive data in reports using NLP techniques and Presidio Analyzer. It offers features like entity flagging, iterative anonymization, and supports multiple model configurations.

GitHub Tools

Repository	Language	Description
template-python-repository		This repository serves as a template for Python projects, providing a structured setup process and guidelines for consistent project organization.
.github		This repository likely serves as a default location for GitHub community health files and templates.
MoBI-Retreat-2024-Collaborative-programming-with-GitHub		This repository contains a presentation on "Collaborative programming with GitHub" for the MoBI Retreat 2024, including video, slides, references, and related materials.
aria-tests		This repository provides a template for Python projects, offering streamlined project setup and a consistent structure. It includes features such as setting up pre-commit hooks, code quality assurance, and API documentation generation.
cloai-service		This repository provides a template for Python projects, offering a structured setup process and guidelines for maintaining consistency. It includes instructions for initializing the repository, setting up code quality checks, and generating API documentation.
ctk-build		This repository automates the building, testing, and deployment process for components of the Clinician Toolkit (CTK) project using GitHub Actions.
beacon		This repository provides a streamlined way to build Svelte projects using the sv tool, offering commands for project creation, development server setup, and production build generation.
ctk-terraform		This repository manages Azure infrastructure for the CTK project using Terraform, organizing it into shared, development, and production environments with a focus on deploying the shared infrastructure first before environment-specific resources.

Neuroimaging Utilities

Repository	Language	Description
bids2table		bids2table is a Python tool that efficiently indexes BIDS datasets, allowing users to quickly search and index datasets locally or in the cloud, with support for S3 storage.
headjack		headjack is an interactive NIfTI image viewer designed for the terminal, offering seamless compatibility with various platforms like remote clusters and containerized environments, making it a valuable tool for researchers and developers.
nifti-stream		nifti-stream is a streaming parser for NIFTI-1 and NIFTI-2 neuroimaging files, optimized for client-side processing and progressive loading in web applications.
C-PAC_slurm_testing		This repository enables C-PAC developers to run full regression tests on Bridges-2 cluster using SLURM job submission scripts.
neurothumb		neurothumb is a Rust-based repository that serves as a neuroimaging file thumbnail generator and integration tool.
tsconcat		This repository provides a BIDS App and Python library for concatenating MRI time series, allowing users to combine BOLD time series from multiple datasets, sessions, subjects, or runs into a single file.
nifti		This repository provides a lightweight NIfTI file reader and writer in C++, utilizing modern zlib for efficient operations.
gen192		gen192 is a Python-based 192 C-PAC pipeline generator that offers various pipelines, pipeline steps, connectivity measures, and nuisance regression options for neuroimaging analysis.
unifti		The "unifti" repository provides minimal header-only NIfTI definitions and utilities in C, capturing NIfTI 1.1 and 2 standard and extension codes, with features like portability, zero heap allocations, and utility functions for NIfTI file handling tasks.
loris-docker		This repository provides Docker builds for Loris, offering different container images with varying dependencies such as Loris, Loris-MRI, and MINC Toolkit, along with instructions for building and configuring the containers efficiently.
MOBI_QC		MOBI_QC is a Python quality control pipeline tailored for assessing multimodal datasets, including EEG, Eye-tracking, Physiological signals, Audio, and Video data. It automates preprocessing, computes detailed quality control metrics for each modality, and generates PDF reports for easy review and documentation.
flowview		FlowView is a Svelte-based C-PAC workflow viewer.
BrainParsers		BrainParsers provides Kaitai struct grammars for parsing various brain imaging data formats.
cpac-log-muncher		This repository provides a Python tool, clmunch, for aggregating and summarizing logs generated by the C-PAC pipeline.
brainviewer-demo		This repository is a demo of the BrainViewer library, allowing users to interact with a brain surface visually and audibly. The brain's zoom and rotation are controlled by the user's microphone input frequencies.
NeuRosetta		NeuRosetta provides GPT-4 translations of common operations in various brain imaging frameworks, aiming to facilitate researchers in switching between and learning different frameworks effortlessly.
bridges-cheatsheet		This repository provides a cheat sheet for efficiently using the Bridges2 compute cluster, including environment variable settings, useful commands for job management, Singularity/Apptainer configurations, Anaconda setup, C-PAC job file templates, and various utilities for enhancing workflow efficiency.
nodeblock-testing		This repository provides testing functionality for C-PAC nodeblocks.
multiecho-processing		This repository contains a Multiecho Preprocessing Pipeline project for processing multiecho fMRI data on C-PAC, providing steps for installation and usage.
skarf		skarf is a Python package for regularized vector autoregressive (VAR) time series modeling, specifically designed for functional connectivity analyses of fMRI data using scikit-learn.
MoBI_Docs		MoBI_Docs is a repository containing materials for the Child Mind Institute's Multimodal Brain/Body Imaging (MoBI) Core, focusing on standardizing research methods and developing software pipelines for data analysis and quality control.
resource-inventory		This repository is a web application that helps users search for resources used in the C-PAC software. It offers a user-friendly interface to browse and search through a comprehensive inventory of resources, with features like search functionality, dark mode, and direct links to specific lines in the GitHub repository.
MoBI-AV		MoBI-AV is a Python application for recording audio and video simultaneously, offering device selection and synchronization capabilities, including integration with Lab Streaming Layer (LSL) for time-synchronizing recordings with other experimental data sources.
MoBI-Markers		A Python GUI application for sending LSL (Lab Streaming Layer) markers used in neuroscience research, featuring a clean interface, real-time marker sending, status logging, and cross-platform compatibility.
neuromaps-prime		The neuromaps-prime repository provides a toolbox for integrating multiscale, multimodal annotations across non-human primate (NHP) brains, facilitating comprehensive comparative brain organization analyses. It extends the neuromaps ecosystem to offer unified access to various NHP brain datasets and specialized tools for NHP-specific analyses.

Python Libraries

Repository	Language	Description
bids2table		bids2table is a Python tool that efficiently indexes BIDS datasets, allowing users to quickly search and index datasets locally or in the cloud, with support for S3 storage.
wristpy		wristpy is a Python package designed for processing and analyzing wrist-worn accelerometer data. It offers tools for loading sensor information, calibrating raw accelerometer data, calculating physical activity metrics, detecting non-wear and sleep periods, and accessing additional sensor data recorded by the watch.
helios-render-kaggle		This repository, helios-render-kaggle, provides a tool for visualizing sensor data from the Helios device, specifically tailored for the CMI - Detect Behavior with Sensor Data competition on Kaggle. It allows users to render sequences from the dataset based on specified filters and generate video files for analysis.
template-python-repository		This repository serves as a template for Python projects, providing a structured setup process and guidelines for consistent project organization.
niftyone		NiftyOne is a platform for bulk visualization of large-scale neuroimaging datasets, utilizing FiftyOne features with popular neuroimaging Python packages.
cmi-docx		cmi-docx is a Python library that enhances the functionality of python-docx for working with .docx files. It offers features like find and replace, inserting paragraphs, and manipulating styles and formatting within documents.
MoBI-View		MoBI-View is a Python GUI application that provides real-time visualization of biosignal data from Lab Streaming Layer (LSL) streams, enabling researchers and clinicians to monitor and analyze various biosignals like EEG and physiological measurements through an intuitive interface.
quick-viz		This repository, "quick-viz," provides short and simple Python visualization scripts to easily generate visualizations for various types of data, such as TSV-stored matrices, Nii-stored 3D brain data, and surface mesh data. The tools are designed to streamline development and testing cycles by offering quick and easy-to-use utilities.
tsconcat		This repository provides a BIDS App and Python library for concatenating MRI time series, allowing users to combine BOLD time series from multiple datasets, sessions, subjects, or runs into a single file.
cross-species-mapper		This repository provides a webapp for translational exploration between humans and macaques, utilizing a Svelte frontend and a Python FastAPI backend.
cloai		Cloai is a command line interface for OpenAI's API that provides a generic interface to large language models, supporting various prompting techniques across different model providers while maintaining a consistent interface.
actfast		actfast is a fast actigraphy data reader for Python, implemented in Rust. It supports reading data from Actigraph GT3X and GENEActiv devices, with planned support for Axivity CWA format.
hbn-ddp		This repository provides a Python preprocessing package, hbn-ddp, designed for handling the Healthy Brain Network clinician consensus diagnostic data. It transforms the data into a more organized format for analysis, allowing filtering by diagnostic certainty or time of diagnosis and creating visualizations of the diagnostic data.
yaspy		yaspy is a Python library for creating neuroimaging surface plots, ranging from simple screenshots to complex montages and publication-ready figures. It leverages PyVista, Matplotlib, and Pillow for its functionality.
gen192		gen192 is a Python-based 192 C-PAC pipeline generator that offers various pipelines, pipeline steps, connectivity measures, and nuisance regression options for neuroimaging analysis.
ctk-functions		This repository contains Azure Functions written in Python for the Clinician Toolkit, offering services such as document conversion, intake form processing, grammatical correction, and text generation through a FastAPI backend.
cpac-callback-plot		This repository provides a Python tool, clplot, for plotting CPAC/Nipype callback logs to visualize a timeline of pipeline events.
mobi-motion-tracking		mobi-motion-tracking is a Python package designed for processing and analyzing 3D motion tracking data. It offers tools to compare skeletal data against a gold standard, calculate similarity metrics like DTW, and generate labeled output files for further analysis.
MOBI_QC		MOBI_QC is a Python quality control pipeline tailored for assessing multimodal datasets, including EEG, Eye-tracking, Physiological signals, Audio, and Video data. It automates preprocessing, computes detailed quality control metrics for each modality, and generates PDF reports for easy review and documentation.
graphomotor		graphomotor is a Python toolkit designed for analyzing graphomotor data collected via Curious, offering feature extraction and visualization capabilities for tasks like spiral drawing, trails making, alphabetic writing, digit symbol substitution, and the Rey-Osterrieth Complex Figure Test.
noctsleepy		noctsleepy is a Python package that computes comprehensive sleep metrics from processed actigraphy data, allowing users to analyze sleep duration, efficiency, wake after sleep onset, and more within customizable nocturnal windows while handling daylight saving time transitions.
synthdata		This repository serves as a sandbox for generating and evaluating synthetic data using Python. It includes tools for data generation, evaluation, and parsing hierarchical structures from markdown documents.
headhunter		headhunter is a Python parser that extracts headings and hierarchical structures from Markdown files, supporting various heading formats, fuzzy matching, batch processing, and export to different formats.
ipyniivue-marimo-test		This repository provides a demo for using ipyniivue marimo, allowing users to open a notebook in edit mode and export it as a WASM+HTML website.
elbow		Elbow is a lightweight Python library designed to transform specialized data into common tabular formats for analytics, offering scalability and ease of use. It allows users to extract diverse data into formats like Parquet for downstream analysis.
flowdump		flowdump is a NiPype workflow serializer designed for use with flowview, allowing users to execute workflows and save pre- and post-execution data to JSON files with ease.
BrainParsers		BrainParsers provides Kaitai struct grammars for parsing various brain imaging data formats.
cpac-log-muncher		This repository provides a Python tool, clmunch, for aggregating and summarizing logs generated by the C-PAC pipeline.
NeuRosetta		NeuRosetta provides GPT-4 translations of common operations in various brain imaging frameworks, aiming to facilitate researchers in switching between and learning different frameworks effortlessly.
survey_subsampling		This repository provides a package for reducing the size of complex survey instruments by identifying and retaining only the most predictive assessment items. It offers a data-driven approach to subsampling surveys like the CBCL based on their ability to predict diagnostic status.
bridges-cheatsheet		This repository provides a cheat sheet for efficiently using the Bridges2 compute cluster, including environment variable settings, useful commands for job management, Singularity/Apptainer configurations, Anaconda setup, C-PAC job file templates, and various utilities for enhancing workflow efficiency.
C-PAC_pre-commit_examples		This repository provides examples of using pre-commit in C-PAC for linting code and making changes in different branches.
nodeblock-testing		This repository provides testing functionality for C-PAC nodeblocks.
aria-tests		This repository provides a template for Python projects, offering streamlined project setup and a consistent structure. It includes features such as setting up pre-commit hooks, code quality assurance, and API documentation generation.
mindlogger-graphomotor-data		This repository parses MindLogger exports in Python using the Bidsi library.
bidsi		Bidsi is a Python library designed to assist in converting various data sources to BIDS format by providing classes and utilities for building and writing BIDS structured data.
multiecho-processing		This repository contains a Multiecho Preprocessing Pipeline project for processing multiecho fMRI data on C-PAC, providing steps for installation and usage.
skarf		skarf is a Python package for regularized vector autoregressive (VAR) time series modeling, specifically designed for functional connectivity analyses of fMRI data using scikit-learn.
MoBI_Docs		MoBI_Docs is a repository containing materials for the Child Mind Institute's Multimodal Brain/Body Imaging (MoBI) Core, focusing on standardizing research methods and developing software pipelines for data analysis and quality control.
doc-bot		The "doc-bot" repository contains the software architecture and cloud deployment details for a chatbot system involving Open WebUI, LiteLLM, and a custom proxy server, with Azure and AWS integrations for storage and processing.
cloai-service		This repository provides a template for Python projects, offering a structured setup process and guidelines for maintaining consistency. It includes instructions for initializing the repository, setting up code quality checks, and generating API documentation.
ctk-build		This repository automates the building, testing, and deployment process for components of the Clinician Toolkit (CTK) project using GitHub Actions.
hbn_correction		This repository provides a Python package for correcting data from the Healthy Brain Network dataset. It offers functionality to perform data corrections and includes a notebook example for reference.
tinyfeast		The "tinyfeast" repository is a Python project with no README file available.
graphomotor_cmi		This repository contains scripts to run the Graphomotor Protocol at the Child Mind Institute during the Summer of 2025. The main script, "graphomotor_full.py," encompasses the entire protocol.
tiny-mirror		This repository, tiny-mirror, provides functionality for generating concerning summaries using Python. It includes methods to obtain both final results and intermediate results for analyzing text entries.
awesome-childmindresearch		This repository is a curated list of 77 active, non-fork public repositories from the Child Mind Institute — Research Teams organization, generated using OpenAI GPT for description and categorization.
MoBI-AV		MoBI-AV is a Python application for recording audio and video simultaneously, offering device selection and synchronization capabilities, including integration with Lab Streaming Layer (LSL) for time-synchronizing recordings with other experimental data sources.
parent-tech-survey		This repository performs text analysis for the PPTOB Study.
zed2i_3d_capture		This repository provides the necessary Python code to record 3D motion tracking data from the ZED 2i stereo camera, enabling real-time body tracking and data collection with or without a live stimulus.
not-as-many-pipelines		This repository provides a diff checker tool for comparing original gen192 configurations with updated ones.
zed2i_3d_lsl_capture		This repository records 3D motion tracking data from the ZED 2i stereo camera and streams live markers to Lab Streaming Layer, saving the data in a format compatible with the mobi_motion_tracking package.
zed2i_motion_classifier		This Python repository, zed2i_motion_classifier, is designed for real-time movement classification using the ZED 2i stereo camera and streams frame-by-frame classifications over LSL (Lab Streaming Layer). It performs action, behavior, and position classification on a single person, streaming these classifications over LSL, and recording video to a .svo2 file.
MoBI-Markers		A Python GUI application for sending LSL (Lab Streaming Layer) markers used in neuroscience research, featuring a clean interface, real-time marker sending, status logging, and cross-platform compatibility.
MoBI-Neon-GUI		MoBI-Neon-GUI is a Python GUI application for recording video from Pupil Labs Neon devices with synchronized LSL markers, offering real-time video preview, recording controls, configurable save directory, and customizable output filenames with timestamp support.
MoBI-Physio-API		A Python API for PLUX biosignals devices with automatic sensor detection and Lab Streaming Layer (LSL) integration, supporting cross-platform usage and real-time data streaming.
helios_eval		This repository provides a tool for evaluating the results of the Helios Kaggle competition using Python.
neuromaps-prime		The neuromaps-prime repository provides a toolbox for integrating multiscale, multimodal annotations across non-human primate (NHP) brains, facilitating comprehensive comparative brain organization analyses. It extends the neuromaps ecosystem to offer unified access to various NHP brain datasets and specialized tools for NHP-specific analyses.
MoBI-Curious-LSL-Relay		This repository, MoBI-Curious-LSL-Relay, is a Python script that serves as an LSL Relay for the Curious app in the context of MoBI. It simplifies the setup process by handling dependencies automatically without the need for manual virtual environment creation or separate package installations.
anonymize-pii		This Python repository provides a text-based PII anonymizer tool that flags and anonymizes sensitive data in reports using NLP techniques and Presidio Analyzer. It offers features like entity flagging, iterative anonymization, and supports multiple model configurations.

Rust Projects

Repository	Language	Description
neurothumb		neurothumb is a Rust-based repository that serves as a neuroimaging file thumbnail generator and integration tool.
actfast		actfast is a fast actigraphy data reader for Python, implemented in Rust. It supports reading data from Actigraph GT3X and GENEActiv devices, with planned support for Axivity CWA format.
ctk-markdown-to-sql		This repository provides a Rust tool for converting hierarchical markdown documents into SQL insertion queries. It parses markdown files into a tree structure and generates SQL commands to insert the parsed data into a database.
cmi-pandoc-server		This repository likely serves as a server application written in Rust for converting documents using Pandoc.
cmi-ffmpeg-server		This repository likely contains a server application written in Rust that utilizes the FFmpeg multimedia framework for various media processing tasks.

Sleep Data Analysis

Repository	Language	Description
wristpy		wristpy is a Python package designed for processing and analyzing wrist-worn accelerometer data. It offers tools for loading sensor information, calibrating raw accelerometer data, calculating physical activity metrics, detecting non-wear and sleep periods, and accessing additional sensor data recorded by the watch.
actisleep-tracker		ActiSleep Tracker is a web application designed for annotating sleep data obtained from actigraphy data processed with the GGIR package. Users can visualize and annotate sleep periods using this tool.
noctsleepy		noctsleepy is a Python package that computes comprehensive sleep metrics from processed actigraphy data, allowing users to analyze sleep duration, efficiency, wake after sleep onset, and more within customizable nocturnal windows while handling daylight saving time transitions.

Visualization Tools

Repository	Language	Description
helios-render-kaggle		This repository, helios-render-kaggle, provides a tool for visualizing sensor data from the Helios device, specifically tailored for the CMI - Detect Behavior with Sensor Data competition on Kaggle. It allows users to render sequences from the dataset based on specified filters and generate video files for analysis.
headjack		headjack is an interactive NIfTI image viewer designed for the terminal, offering seamless compatibility with various platforms like remote clusters and containerized environments, making it a valuable tool for researchers and developers.
niftyone		NiftyOne is a platform for bulk visualization of large-scale neuroimaging datasets, utilizing FiftyOne features with popular neuroimaging Python packages.
MoBI-View		MoBI-View is a Python GUI application that provides real-time visualization of biosignal data from Lab Streaming Layer (LSL) streams, enabling researchers and clinicians to monitor and analyze various biosignals like EEG and physiological measurements through an intuitive interface.
quick-viz		This repository, "quick-viz," provides short and simple Python visualization scripts to easily generate visualizations for various types of data, such as TSV-stored matrices, Nii-stored 3D brain data, and surface mesh data. The tools are designed to streamline development and testing cycles by offering quick and easy-to-use utilities.
brainviewer		BrainViewer is a tool for scientific visualization of 3D mesh data in JavaScript/TypeScript, built on ThreeJS, providing a fast and responsive interface for visualizing 3D meshes in the browser.
hbn-ddp		This repository provides a Python preprocessing package, hbn-ddp, designed for handling the Healthy Brain Network clinician consensus diagnostic data. It transforms the data into a more organized format for analysis, allowing filtering by diagnostic certainty or time of diagnosis and creating visualizations of the diagnostic data.
yaspy		yaspy is a Python library for creating neuroimaging surface plots, ranging from simple screenshots to complex montages and publication-ready figures. It leverages PyVista, Matplotlib, and Pillow for its functionality.
cpac-callback-plot		This repository provides a Python tool, clplot, for plotting CPAC/Nipype callback logs to visualize a timeline of pipeline events.
mobi-motion-tracking		mobi-motion-tracking is a Python package designed for processing and analyzing 3D motion tracking data. It offers tools to compare skeletal data against a gold standard, calculate similarity metrics like DTW, and generate labeled output files for further analysis.
graphomotor		graphomotor is a Python toolkit designed for analyzing graphomotor data collected via Curious, offering feature extraction and visualization capabilities for tasks like spiral drawing, trails making, alphabetic writing, digit symbol substitution, and the Rey-Osterrieth Complex Figure Test.
flowview		FlowView is a Svelte-based C-PAC workflow viewer.
vmi-train		This repository provides a generic configurable mobile task designed to track objects using ShaderLab.
brainviewer-demo		This repository is a demo of the BrainViewer library, allowing users to interact with a brain surface visually and audibly. The brain's zoom and rotation are controlled by the user's microphone input frequencies.
zed2i_3d_capture		This repository provides the necessary Python code to record 3D motion tracking data from the ZED 2i stereo camera, enabling real-time body tracking and data collection with or without a live stimulus.
MoBI-Neon-GUI		MoBI-Neon-GUI is a Python GUI application for recording video from Pupil Labs Neon devices with synchronized LSL markers, offering real-time video preview, recording controls, configurable save directory, and customizable output filenames with timestamp support.

Web Applications

Repository	Language	Description
nifti-stream		nifti-stream is a streaming parser for NIFTI-1 and NIFTI-2 neuroimaging files, optimized for client-side processing and progressive loading in web applications.
cross-species-mapper		This repository provides a webapp for translational exploration between humans and macaques, utilizing a Svelte frontend and a Python FastAPI backend.
brainviewer		BrainViewer is a tool for scientific visualization of 3D mesh data in JavaScript/TypeScript, built on ThreeJS, providing a fast and responsive interface for visualizing 3D meshes in the browser.
actisleep-tracker		ActiSleep Tracker is a web application designed for annotating sleep data obtained from actigraphy data processed with the GGIR package. Users can visualize and annotate sleep periods using this tool.
cloai		Cloai is a command line interface for OpenAI's API that provides a generic interface to large language models, supporting various prompting techniques across different model providers while maintaining a consistent interface.
ctk-webapp		This repository contains the frontend code for the Clinician Toolkit, a SvelteKit application deployed as a Docker container, part of a larger set of Clinician Toolkit repositories.
ctk-functions		This repository contains Azure Functions written in Python for the Clinician Toolkit, offering services such as document conversion, intake form processing, grammatical correction, and text generation through a FastAPI backend.
ipyniivue-marimo-test		This repository provides a demo for using ipyniivue marimo, allowing users to open a notebook in edit mode and export it as a WASM+HTML website.
brainviewer-demo		This repository is a demo of the BrainViewer library, allowing users to interact with a brain surface visually and audibly. The brain's zoom and rotation are controlled by the user's microphone input frequencies.
MoBI-Retreat-2024-Collaborative-programming-with-GitHub		This repository contains a presentation on "Collaborative programming with GitHub" for the MoBI Retreat 2024, including video, slides, references, and related materials.
cmi-skeleton-themes		This repository provides a CSS Skeleton theme specifically designed for the Child Mind Institute, allowing easy integration into web projects by following simple installation and import instructions.
cmi-pandoc-server		This repository likely serves as a server application written in Rust for converting documents using Pandoc.
doc-bot		The "doc-bot" repository contains the software architecture and cloud deployment details for a chatbot system involving Open WebUI, LiteLLM, and a custom proxy server, with Azure and AWS integrations for storage and processing.
blockbuster		The "blockbuster" repository contains HTML code for a BlockBuster project.
resource-inventory		This repository is a web application that helps users search for resources used in the C-PAC software. It offers a user-friendly interface to browse and search through a comprehensive inventory of resources, with features like search functionality, dark mode, and direct links to specific lines in the GitHub repository.
MoBI-Physio-API		A Python API for PLUX biosignals devices with automatic sensor detection and Lab Streaming Layer (LSL) integration, supporting cross-platform usage and real-time data streaming.
beacon		This repository provides a streamlined way to build Svelte projects using the sv tool, offering commands for project creation, development server setup, and production build generation.

About this list

This awesome list is automatically generated weekly using a GitHub Action. Last updated: 2026-02-09 00:06:34 UTC

In this update: 40 repositories (48%) were served from cache, and 43 repositories were freshly analyzed.