{"id": "package:34c01896-fcc0-4c5b-b386-fc3d28a95a62", "name": "README.md", "self_uri": "https://services.scicrunch.io/sparc/drs/v1/objects/34c01896-fcc0-4c5b-b386-fc3d28a95a62", "size": 1564, "created_time": "2025-09-24T22:00:58,020120Z", "updated_time": "2025-09-24T22:02:32,989240Z", "version": "1", "mime_type": "text/markdown", "checksums": [{"checksum": "65c1cc6aad91eceecbefe6cecbc12587", "type": "sha256"}], "access_methods": [{"type": "s3", "access_url": {"url": "s3://prod-rejoin-discover50-use1/469/files/README.md"}, "region": "us-east-1"}], "dataset": {"id": "469", "doi": "DOI:10.26275/64i6-wdv0", "title": "Image processing and analysis protocol for fluorescent calcium imaging ", "description": "A comprehensive automated pipeline for analyzing fluorescent calcium imaging data, providing motion correction, signal processing, and quality control for neuroscience research.", "abstract": "Calcium Imaging Analysis Protocol\nProject: HEAL RE-JOIN\n\nSummary. The Calcium Imaging Analysis Protocol is an automated software pipeline that integrates MATLAB and ImageJ to streamline the analysis of fluorescent calcium imaging data. This toolkit provides motion correction, signal processing, and quality control, reducing weeks of manual analysis to hours while generating publication-ready visualizations.\n\nKey features\n\nAutomated motion correction (MATLAB)\n\nSignal processing with bleach correction & neuropil subtraction\n\nQC with semi-automated thresholding and ROI management (ImageJ/FIJI)\n\nΔF/F, AUC, heatmaps, and exportable statistics\n\nRequirements\n\nMATLAB R2024b (Image Processing, Curve Fitting toolboxes)\n\nFIJI (ImageJ)\n\nOS: Windows 10/11, macOS 10.15+, or Ubuntu 18.04+\n\nHow to use (quick start\n\nInstall MATLAB + toolboxes and FIJI\n\nClone/download the repo and add folders to the MATLAB path\n\nRun Correct_movements.m → main_neurop_sub.m → QC via Thresholding.mlapp\n\nExport traces/plots from the provided scripts\n\nCitation Calcium Imaging Analysis Protocol v1.0, Joshua Emric Lab, DOI: https://doi.org/10.26275/rdas-u8z4\n\nLicense & contact Academic Research License. For support/collaboration: Joshua Emric Laboratory."}}