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Section 1: Foundations of Calcium Signaling and Fluorescent Reporters

Why Calcium Imaging Matters

What Calcium Imaging Is — and Is Not

From Electrical Activity to Fluorescence

Section 2: Engineering and Diversity of Calcium Indicators

Chemical Calcium Indicators

Genetically Encoded Calcium Indicators

Fast and Multicolor Indicators

Section 3: Imaging Modalities and Hardware Platforms

Two-Photon Calcium Imaging

Wide-Field and Mesoscale Imaging

Miniscopes and Freely Moving Imaging

Fiber Photometry

Section 4: Subcellular Specificity and Experimental Artifacts

Subcellular and Targeted Indicators

Motion, Neuropil, and Hemodynamic Artifacts

Photobleaching, Phototoxicity, and Thermal Artifacts

Section 5: Data Processing, Signal Inference, and Validation

Signal Processing and Spike Inference

Evidence: What Counts as Strong Enough?

Translation Barriers

Section 6: Critical Evaluation and Decision Frameworks

What Stakeholders Should Ask

Case Scenarios and Decision Frameworks

Section 7: Knowledge Assessment Quizzes

Quiz 1: Fundamentals of Calcium Signaling

Quiz 2: Sensor Dynamics and Kinetics

Quiz 3: Chemical and Genetically Encoded Indicators

Quiz 4: Advanced GECIs and Multicolor Imaging

Quiz 5: Multiphoton and Wide-Field Microscopy

Quiz 6: Miniscopes and Freely Moving Systems

Quiz 7: Fiber Photometry Limitations

Quiz 8: Artifacts and Neuropil Contamination

Quiz 9: Spike Inference and Signal Processing

Quiz 10: Experimental Validation and Translation

Section 8: Course Evaluation Surveys

Survey 1: Foundations Module Feedback

Survey 2: Sensor Diversity Module Feedback

Survey 3: Advanced GECIs Module Feedback

Survey 4: Microscopy Modalities Module Feedback

Survey 5: Freely Moving Systems Module Feedback

Survey 6: Artifacts and Contamination Module Feedback

Survey 7: Signal Processing Module Feedback

Survey 8: Validation Frameworks Module Feedback

Survey 9: Stakeholder Evaluation Module Feedback

Survey 10: Overall Course Effectiveness and Application Feedback

Welcome to "Calcium Imaging in Neuroscience: Techniques, Analysis, and Interpretation," the definitive online course designed to elevate your understanding of one of the most powerful tools in modern systems neuroscience. Whether you are a graduate student, a postdoctoral researcher, or a seasoned neurobiologist, mastering calcium imaging is essential for decoding the complex dynamics of neural circuits.

Welcome to "Calcium Imaging in Neuroscience: Techniques, Analysis, and Interpretation," the definitive online course designed to elevate your understanding of one of the most powerful tools in modern systems neuroscience. Whether you are a graduate student, a postdoctoral researcher, or a seasoned neurobiologist, mastering calcium imaging is essential for decoding the complex dynamics of neural circuits. This comprehensive course bridges the gap between fundamental biophysics and advanced computational analysis.

You will explore the physiological roles of calcium in neuronal signaling and learn how to translate electrical activity into observable fluorescence signals. We dive deep into the engineering of chemical and genetically encoded calcium indicators (GECIs), including the latest fast and multicolor variants like jGCaMP8. Beyond the sensors, you will evaluate cutting-edge imaging modalities, from two-photon microscopy and wide-field mesoscale imaging to freely moving miniscopes and fiber photometry.

Crucially, this course doesn't just teach you how to acquire data; it teaches you how to interpret it rigorously. You will learn to identify and mitigate experimental artifacts—such as neuropil contamination, motion, and phototoxicity—and master the computational algorithms used for signal processing and spike inference. By the end of this program, you will possess a robust decision framework to critically evaluate calcium imaging data, ensuring your research findings are biologically relevant, statistically sound, and ready for high-impact publication. Join us to transform raw fluorescence into profound neurobiological insights.

64. Calcium Imaging in Neuroscience: Techniques, Analysis, and Interpretation

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            <p>Calcium imaging has fundamentally transformed systems neuroscience by enabling the large-scale, optical observation of neural circuit dynamics in vivo. This course provides a comprehensive examination of the biophysical principles, technological advancements, and analytical frameworks that underpin this powerful methodology. Beginning with the foundational relationship between intracellular calcium signaling and observable fluorescence, the curriculum systematically explores the complex translation of electrical action potentials into optical signals. Participants will critically evaluate the engineering and diversity of both chemical and genetically encoded calcium indicators (GECIs), analyzing how specific molecular designs dictate binding affinity, temporal resolution, and signal-to-noise performance across various experimental paradigms.</p>

<p>Beyond the molecular tools, the successful application of calcium imaging requires a rigorous understanding of diverse imaging modalities and the inherent challenges of in vivo data acquisition. The course meticulously dissects hardware platforms ranging from two-photon and wide-field microscopy to freely moving miniscopes and fiber photometry, highlighting the distinct advantages and limitations of each approach. Furthermore, it addresses critical experimental barriers, including motion artifacts, neuropil contamination, and phototoxicity, while providing robust strategies for signal processing and spike inference. By culminating in advanced decision frameworks and stakeholder evaluation criteria, this program equips researchers, computational scientists, and neurotechnology developers with the analytical rigor necessary to validate fluorescence data, ensure reproducibility, and accurately interpret complex neural population codes.</p>
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