Neural Data Analysis

Tests make scientific assumptions and expected behavior explicit, and help catch regressions as analysis code develops.

Covered in our robust software and AI-assisted development topics; individual offerings are not yet attributed to this practice.

0 past offerings · 0 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: AI-Assisted Software DevelopmentMachine Learning(M)EEG AnalysisNeural Spike AnalysisRobust and Reusable Software

Explicit validation turns data assumptions into checks that can catch missing values, inconsistent metadata, and unexpected inputs before analysis.

Covered through data organization and robust software topics; individual offerings are not yet attributed to this practice.

0 past offerings · 0 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: Programming and Data AcquisitionAI-Assisted Software DevelopmentArrays and Numerical ComputingCalcium Imaging AnalysisDataframes and StatisticsLocal Field Potential (LFP) AnalysisMachine Learning(M)EEG AnalysisNeural Spike AnalysisRobust and Reusable Software

HDF5 is the standard format for storing large, complex scientific datasets with rich metadata. Its hierarchical structure and efficient compression make it ideal for neuroscience data like multi-channel recordings and imaging time series.

Relevant to the topic landscape; no explicit recorded offering is currently attributed to this item.

0 past offerings · 0 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: Arrays and Numerical ComputingCalcium Imaging AnalysisDataframes and Statistics(M)EEG Analysis

Matplotlib is the foundational plotting library for Python, offering complete control over every aspect of your figures. It's publication-ready out of the box and integrates seamlessly with NumPy and Pandas, making it essential for visualizing research data.

Recorded in topic offerings; consult the dated event links for availability.

15 past offerings · 4 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: AI-Assisted Software DevelopmentArrays and Numerical ComputingDataframes and StatisticsDeveloper EnvironmentLocal Field Potential (LFP) Analysis(M)EEG AnalysisNeural Spike Analysis

MNE-Python provides a comprehensive, well-documented toolkit for processing electrophysiological data. It handles the full analysis pipeline from raw recordings to publication-ready results, with strong support for time-frequency analysis, source localization, and connectivity measures.

Recorded in topic offerings; consult the dated event links for availability.

2 past offerings · 1 upcoming offerings

Related themes: Neural Data Analysis

Related topics: Local Field Potential (LFP) Analysis(M)EEG Analysis

NumPy is the foundation of the scientific Python ecosystem. It provides powerful n-dimensional array objects and tools for working with these arrays. Nearly every scientific Python package builds on NumPy, making it essential for data analysis, numerical computing, and scientific research.

Recorded in topic offerings; consult the dated event links for availability.

21 past offerings · 5 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: AI-Assisted Software DevelopmentArrays and Numerical ComputingCalcium Imaging AnalysisDataframes and StatisticsLocal Field Potential (LFP) AnalysisMachine Learning(M)EEG AnalysisNeural Spike AnalysisRobust and Reusable Software

NWB is the emerging standard for neuroscience data sharing, required by many NIH BRAIN Initiative grants. It provides a unified format for diverse data types (ephys, imaging, behavior) with rich metadata, enabling tool interoperability and compliance with FAIR principles.

Relevant to the topic landscape; no explicit recorded offering is currently attributed to this item.

0 past offerings · 0 upcoming offerings

Related themes: Neural Data Analysis

Related topics: Calcium Imaging AnalysisLocal Field Potential (LFP) Analysis(M)EEG AnalysisNeural Spike Analysis

Pandas provides intuitive data structures (DataFrames) for working with tabular data, making it easy to clean, analyze, and visualize datasets. It's the go-to tool for exploratory data analysis and handling experimental results in research.

Recorded in topic offerings; consult the dated event links for availability.

14 past offerings · 2 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: AI-Assisted Software DevelopmentArrays and Numerical ComputingAutomating Research WorkflowsDataframes and StatisticsLocal Field Potential (LFP) AnalysisNeural Spike Analysis

Python combines a readable language with a mature scientific ecosystem, making it a practical default for research data analysis, automation, and teaching.

Recorded in topic offerings; consult the dated event links for availability.

26 past offerings · 7 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: Programming and Data AcquisitionAI-Assisted Software DevelopmentArrays and Numerical ComputingAutomating Research WorkflowsCalcium Imaging AnalysisDataframes and StatisticsDeveloper EnvironmentLocal Field Potential (LFP) AnalysisMachine Learning(M)EEG AnalysisNeural Spike AnalysisRobust and Reusable Software

Declared dependencies and lock files help collaborators rerun analyses and distinguish environment changes from changes in scientific results.

Covered through our computing environment and research workflow topics; individual offerings are not yet attributed to this practice.

0 past offerings · 0 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: AI-Assisted Software DevelopmentArrays and Numerical ComputingAutomating Research WorkflowsCalcium Imaging AnalysisDataframes and StatisticsDeveloper EnvironmentLocal Field Potential (LFP) AnalysisMachine LearningRobust and Reusable Software

Scikit-image provides a comprehensive collection of image processing algorithms that are essential for microscopy and biological imaging. It's well-documented, actively maintained, and integrates seamlessly with NumPy and other scientific Python tools.

Recorded in topic offerings; consult the dated event links for availability.

4 past offerings · 1 upcoming offerings

Related themes: Neural Data Analysis

Related topics: Calcium Imaging Analysis

Scikit-learn provides a consistent, easy-to-use interface for machine learning in Python. It's perfect for analyzing neuroscience data: clustering neurons, reducing dimensionality of neural responses, and classifying behavioral states.

Recorded in topic offerings; consult the dated event links for availability.

4 past offerings · 2 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: AI-Assisted Software DevelopmentMachine Learning(M)EEG AnalysisNeural Spike Analysis

SciPy builds on NumPy to provide a comprehensive collection of algorithms for scientific computing. Its signal processing tools are essential for analyzing neural recordings, while its optimization and statistical functions support data analysis and modeling across neuroscience research.

Recorded in topic offerings; consult the dated event links for availability.

9 past offerings · 5 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: AI-Assisted Software DevelopmentArrays and Numerical ComputingCalcium Imaging AnalysisLocal Field Potential (LFP) AnalysisMachine Learning(M)EEG AnalysisNeural Spike Analysis

SpikeInterface provides a single, unified interface to run and compare multiple spike sorting algorithms. It standardizes the spike sorting workflow from preprocessing through quality metrics, making it easier to process extracellular recordings.

Recorded in topic offerings; consult the dated event links for availability.

2 past offerings · 1 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: AI-Assisted Software DevelopmentNeural Spike Analysis

CaImAn provides state-of-the-art algorithms for processing calcium imaging movies. It handles motion correction, source extraction, and deconvolution in a unified pipeline, making it the standard tool for extracting neural activity from two-photon and one-photon imaging data.

Recorded in topic offerings; consult the dated event links for availability.

2 past offerings · 0 upcoming offerings

Related themes: Neural Data Analysis

Related topics: Calcium Imaging Analysis

The EBRAINS Collaboratory combines hosted JupyterLab, shared storage, documentation, and team management in workspaces designed for neuroscience. It is worth exploring when a course or project needs a shared cloud environment with direct access to EBRAINS tools and resources.

Recorded in scheduled neuroscience offerings; consult the dated event links for availability.

0 past offerings · 1 upcoming offerings

Related themes: Neural Data Analysis

Related topics: Calcium Imaging AnalysisNeural Spike Analysis

Elephant provides a comprehensive suite of analysis methods specifically designed for electrophysiology data. It handles spike trains, continuous signals, and their relationships with proper units and data structures, making complex analyses reproducible and standardized.

Recorded in topic offerings; consult the dated event links for availability.

3 past offerings · 2 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: AI-Assisted Software DevelopmentLocal Field Potential (LFP) AnalysisNeural Spike Analysis

fsspec provides a single, consistent interface for working with files whether they're on your local disk, in the cloud, or on GitHub. This means you can write code once and access data from multiple sources without changing your file operations.

Recorded in topic offerings; consult the dated event links for availability.

0 past offerings · 1 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: Automating Research WorkflowsCalcium Imaging AnalysisDataframes and Statistics

h5py gives Python users direct access to hierarchical HDF5 datasets, including partial reads and structured metadata, which are important for large scientific data files.

Recorded in topic offerings; consult the dated event links for availability.

1 past offerings · 1 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: Arrays and Numerical ComputingCalcium Imaging AnalysisDataframes and StatisticsRobust and Reusable Software

LFPy connects multicompartment NEURON models with predictions of extracellular potentials and other observable signals. It is worth exploring when an analysis needs to relate cellular or network activity to simulated electrode measurements while keeping the biophysical assumptions explicit.

Recorded in a scheduled local-field-potential offering; consult the dated event link for availability.

0 past offerings · 1 upcoming offerings

Related themes: Neural Data Analysis

Related topics: Local Field Potential (LFP) Analysis

Napari provides an intuitive, fast viewer for multi-dimensional scientific images. It's perfect for exploring calcium imaging data, manually selecting ROIs, and visualizing complex image stacks. Its plugin ecosystem and Python API make it both user-friendly and extensible.

Recorded in topic offerings; consult the dated event links for availability.

3 past offerings · 0 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: Arrays and Numerical ComputingCalcium Imaging Analysis

Neo provides standardized data structures for electrophysiology that bridge different recording systems and analysis tools. It handles metadata, units, and relationships between data types, making your analysis code more portable and maintainable.

Recorded in topic offerings; consult the dated event links for availability.

1 past offerings · 0 upcoming offerings

Related themes: Neural Data Analysis

Related topics: Calcium Imaging AnalysisLocal Field Potential (LFP) Analysis(M)EEG AnalysisNeural Spike Analysis

Polars is useful when tabular workflows need more speed, lower memory use, or lazy query planning while remaining approachable for Python users.

Recorded in topic offerings; consult the dated event links for availability.

1 past offerings · 0 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: Dataframes and StatisticsNeural Spike AnalysisRobust and Reusable Software

ProbeInterface provides a standardized way to describe electrode probe geometries (Neuropixels, tetrodes, etc.). It handles the complex spatial layouts and wiring of modern high-density probes, making it easier to visualize and analyze multi-channel recordings.

Relevant to the topic landscape; no explicit recorded offering is currently attributed to this item.

0 past offerings · 0 upcoming offerings

Related themes: Neural Data Analysis

Related topics: Neural Spike Analysis

SciPy Stats provides a broad, scriptable foundation for distributions, statistical tests, random variables, and summary statistics used throughout scientific Python workflows.

Recorded in topic offerings; consult the dated event links for availability.

0 past offerings · 1 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: Arrays and Numerical ComputingDataframes and StatisticsLocal Field Potential (LFP) Analysis(M)EEG Analysis

siibra provides structured programmatic access to integrated brain atlases, including the Allen Mouse Common Coordinate Framework used in atlas-registration workflows. It is worth exploring when analyses need reproducible region assignment or access to anatomically anchored data.

Recorded in a scheduled calcium-imaging offering; consult the dated event link for availability.

0 past offerings · 1 upcoming offerings

Related themes: Neural Data Analysis

Related topics: Calcium Imaging Analysis

Suite2p provides a complete, automated pipeline for calcium imaging analysis from raw TIFF files to extracted neural activity traces. Its GUI makes it accessible for beginners while its Python API enables advanced customization and batch processing.

Recorded in topic offerings; consult the dated event links for availability.

2 past offerings · 1 upcoming offerings

Related themes: Neural Data Analysis

Related topics: Calcium Imaging Analysis

Tifffile is the most reliable and feature-rich library for working with TIFF files in scientific imaging. It handles complex multi-page TIFF stacks, OME-TIFF metadata, and BigTIFF formats that are standard in microscopy.

Relevant to the topic landscape; no explicit recorded offering is currently attributed to this item.

0 past offerings · 0 upcoming offerings

Related themes: Neural Data Analysis

Related topics: Calcium Imaging Analysis

Xarray extends pandas-like labels and indexing to multi-dimensional arrays, making it perfect for working with complex scientific datasets like electrophysiology recordings, imaging data, and climate data. It handles coordinates, dimensions, and metadata elegantly.

Recorded in topic offerings; consult the dated event links for availability.

1 past offerings · 1 upcoming offerings

Related themes: Neural Data AnalysisScientific Computing

Related topics: Arrays and Numerical ComputingDataframes and Statistics(M)EEG AnalysisRobust and Reusable Software

Assess whether this fits the group’s research and teaching workflows. mTRFpy brings temporal response function modeling to Python. It supports regularized forward and backward models, cross-validation, prediction, visualization, and integration with MNE-Python, making it well suited to reproducible analyses of continuous neurophysiological data.

Recorded in topic offerings; consult the dated event links for availability.

1 past offerings · 1 upcoming offerings

Related themes: Neural Data Analysis

Related topics: (M)EEG Analysis