This topic covers the path from raw calcium imaging movies to extracted fluorescence signals and inferred neural activity. You will learn to process raw movies, correct motion, identify regions of interest (ROIs), extract fluorescence traces, account for neuropil contamination, and infer spiking activity through deconvolution. Using real calcium imaging data, you will connect the foundations of image and signal processing to practical workflows for cell detection and classification, reproducible pipeline development, multi-day cell tracking, and atlas registration.
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Calcium imaging produces movies in which changes in fluorescence provide an indirect measure of neural activity. Transforming raw movies into interpretable signals involves motion correction, region selection, trace extraction, neuropil correction, and careful interpretation of the relationship between fluorescence and neural spiking.
Calcium imaging analysis involves a chain of interdependent decisions, including file conversion, downsampling, motion correction, segmentation, neuropil correction, trace extraction, and quality control. Each decision affects subsequent results and what can be interpreted from them. This topic helps you understand the full workflow, compare open-source tools, and document analysis choices so that results remain traceable from raw movies to final figures.
For this approach, familiarity with Python and Jupyter notebooks is required. Consult the event page for its specific setup and requirements.
Using real 2-photon calcium imaging data and Python tools such as NumPy, SciPy, Napari, and Suite2p, you will correct motion, identify regions of interest manually and automatically, extract fluorescence traces, and account for signals from the surrounding neuropil. You will also work with whole-brain imaging data to analyze population-level signals and compute event-related activity maps to relate these data to stimuli.
Building on these methods, you will combine the steps into automated, reproducible pipelines for cell detection and classification, track cells across multi-day recordings with Track2p, and use Siibra-Python to register imaging data to the Allen Mouse Brain Atlas, assess anatomical alignment, and assign cells to brain regions.
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This four-week online course covers analyzing two-photon and widefield calcium imaging data in Python, from fluorescence extraction, spike inference, ROI selection, automated …
Customized programming workshops for lab retreats, department events, and group training
Introduction to analysis of calcium imaging data with CaImAn
Customized programming workshops for lab retreats, department events, and group training
Analysis of calcium imaging data with CaImAn
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Check the shape, types, units, and assumptions of research data before using it.
Practices · Teaching
0 topics with recorded teaching · 0 recorded and scheduled offerings
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
Hierarchical Data Format for storing large scientific datasets
Data formats · Not currently taught
0 topics with recorded teaching · 0 recorded and scheduled offerings
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
The fundamental package for scientific computing with Python
Libraries · Teaching
8 topics with recorded teaching · 26 recorded and scheduled offerings
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
Standardized format for neuroscience data sharing and archival
Data formats · Not currently taught
0 topics with recorded teaching · 0 recorded and scheduled offerings
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
General-purpose programming language widely used for scientific computing and research software.
Languages & frameworks · Teaching
10 topics with recorded teaching · 33 recorded and scheduled offerings
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
Record and reproduce the software environment used for an analysis or application.
Practices · Teaching
0 topics with recorded teaching · 0 recorded and scheduled offerings
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
Image processing library for Python providing algorithms for segmentation, filtering, and analysis
Libraries · Teaching
1 topics with recorded teaching · 5 recorded and scheduled offerings
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
Scientific computing library providing optimization, signal processing, and statistical functions
Libraries · Teaching
5 topics with recorded teaching · 14 recorded and scheduled offerings
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
Computational toolbox for calcium imaging data analysis
Tools & platforms · Teaching
1 topics with recorded teaching · 2 recorded and scheduled offerings
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
Cloud workspace for collaborative neuroscience projects, combining hosted JupyterLab, shared storage, documentation, and communication services
Tools & platforms · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
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
Unified filesystem interface for Python providing consistent API across local and remote storage
Libraries · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
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
Python interface for reading and writing HDF5 files.
Libraries · Teaching
2 topics with recorded teaching · 2 recorded and scheduled offerings
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
Multi-dimensional image viewer for Python with interactive visualization and annotation capabilities
Tools & platforms · Teaching
1 topics with recorded teaching · 3 recorded and scheduled offerings
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
Python package for working with electrophysiology data, providing common data structures and I/O for various formats
Libraries · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
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
Open software toolkit for exploring brain atlases and integrating parcellations, reference spaces, and anatomically anchored data into neuroscience workflows
Libraries · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
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
Fast, accurate, and automated pipeline for processing two-photon calcium imaging data
Tools & platforms · Teaching
1 topics with recorded teaching · 3 recorded and scheduled offerings
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
Python library for reading and writing TIFF files, including OME-TIFF microscopy images
Libraries · Not currently taught
0 topics with recorded teaching · 0 recorded and scheduled offerings
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
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