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| 1 | +{ |
| 2 | + "repo_notes": [ |
| 3 | + { |
| 4 | + "content": "Suite2p is a complete processing pipeline for neural imaging", |
| 5 | + "author": "Carsen Stringer & Marius Pachitariu" |
| 6 | + } |
| 7 | + ], |
| 8 | + "pages": [ |
| 9 | + { |
| 10 | + "title": "Overview", |
| 11 | + "purpose": "High-level overview of suite2p's imaging pipeline and how db, settings etc interact" |
| 12 | + }, |
| 13 | + { |
| 14 | + "title": "Installation and Setup", |
| 15 | + "purpose": "How to install suite2p and configure the environment", |
| 16 | + "parent": "Overview" |
| 17 | + }, |
| 18 | + { |
| 19 | + "title": "Core Concepts", |
| 20 | + "purpose": "Foundational concepts including pipeline architecture, configuration, and data formats" |
| 21 | + }, |
| 22 | + { |
| 23 | + "title": "Pipeline Architecture", |
| 24 | + "purpose": "How the processing stages connect: registration, detection, extraction, deconvolution, classification", |
| 25 | + "parent": "Core Concepts" |
| 26 | + }, |
| 27 | + { |
| 28 | + "title": "Configuration (db and settings)", |
| 29 | + "purpose": "The db dictionary and settings dictionary, and all configurable parameters for controlling pipeline behavior", |
| 30 | + "parent": "Core Concepts" |
| 31 | + }, |
| 32 | + { |
| 33 | + "title": "Data Structures and File Formats", |
| 34 | + "purpose": "Input file formats (tiff, h5, sbx, etc.) and output files (stat.npy, F.npy, iscell.npy, etc.)", |
| 35 | + "parent": "Core Concepts" |
| 36 | + }, |
| 37 | + { |
| 38 | + "title": "Processing Pipeline", |
| 39 | + "purpose": "Detailed documentation of each processing stage in the suite2p pipeline" |
| 40 | + }, |
| 41 | + { |
| 42 | + "title": "Data Input and Conversion", |
| 43 | + "purpose": "How raw imaging data is loaded, converted to binary format, and prepared for processing", |
| 44 | + "parent": "Processing Pipeline" |
| 45 | + }, |
| 46 | + { |
| 47 | + "title": "Registration (Motion Correction)", |
| 48 | + "purpose": "Rigid and nonrigid registration methods for correcting motion artifacts in imaging data", |
| 49 | + "parent": "Processing Pipeline" |
| 50 | + }, |
| 51 | + { |
| 52 | + "title": "ROI Detection", |
| 53 | + "purpose": "How regions of interest (neurons) are detected using sparse decomposition and clustering", |
| 54 | + "parent": "Processing Pipeline" |
| 55 | + }, |
| 56 | + { |
| 57 | + "title": "Signal Extraction and Deconvolution", |
| 58 | + "purpose": "Extracting fluorescence traces from ROIs, neuropil subtraction, and spike deconvolution via OASIS", |
| 59 | + "parent": "Processing Pipeline" |
| 60 | + }, |
| 61 | + { |
| 62 | + "title": "Cell Classification", |
| 63 | + "purpose": "Classifier that distinguishes cells from non-cell ROIs using shape and activity features", |
| 64 | + "parent": "Processing Pipeline" |
| 65 | + }, |
| 66 | + { |
| 67 | + "title": "User Interfaces", |
| 68 | + "purpose": "The different ways to run and interact with suite2p" |
| 69 | + }, |
| 70 | + { |
| 71 | + "title": "Command-Line Interface", |
| 72 | + "purpose": "Running suite2p from the command line with arguments and config files", |
| 73 | + "parent": "User Interfaces" |
| 74 | + }, |
| 75 | + { |
| 76 | + "title": "Python API", |
| 77 | + "purpose": "Using suite2p programmatically in Python scripts and notebooks", |
| 78 | + "parent": "User Interfaces" |
| 79 | + }, |
| 80 | + { |
| 81 | + "title": "Graphical User Interface", |
| 82 | + "purpose": "The PyQt-based GUI for running suite2p and visualizing results", |
| 83 | + "parent": "User Interfaces" |
| 84 | + }, |
| 85 | + { |
| 86 | + "title": "Main Visualization GUI", |
| 87 | + "purpose": "Visualizing ROIs, traces, and registration results in the main GUI window", |
| 88 | + "parent": "Graphical User Interface" |
| 89 | + }, |
| 90 | + { |
| 91 | + "title": "Run Configuration Window", |
| 92 | + "purpose": "Setting parameters and file paths through the GUI run dialog", |
| 93 | + "parent": "Graphical User Interface" |
| 94 | + }, |
| 95 | + { |
| 96 | + "title": "Advanced Topics", |
| 97 | + "purpose": "Multi-plane recordings, distributed processing, and data format integrations" |
| 98 | + }, |
| 99 | + { |
| 100 | + "title": "Multi-Plane and Multi-Channel Processing", |
| 101 | + "purpose": "Handling multi-plane (volumetric) and multi-channel imaging sessions, including multi-day alignment", |
| 102 | + "parent": "Advanced Topics" |
| 103 | + }, |
| 104 | + { |
| 105 | + "title": "Distributed Processing", |
| 106 | + "purpose": "Running suite2p across multiple machines or in parallel for large datasets", |
| 107 | + "parent": "Advanced Topics" |
| 108 | + }, |
| 109 | + { |
| 110 | + "title": "NWB Integration", |
| 111 | + "purpose": "Reading and writing Neurodata Without Borders (NWB) format files", |
| 112 | + "parent": "Advanced Topics" |
| 113 | + }, |
| 114 | + { |
| 115 | + "title": "Development", |
| 116 | + "purpose": "Contributing to suite2p, package structure, and testing" |
| 117 | + }, |
| 118 | + { |
| 119 | + "title": "Package Structure", |
| 120 | + "purpose": "Organization of the suite2p codebase: modules, subpackages, and their responsibilities", |
| 121 | + "parent": "Development" |
| 122 | + }, |
| 123 | + { |
| 124 | + "title": "Testing Framework", |
| 125 | + "purpose": "How tests are structured, regression tests, and how to run the test suite", |
| 126 | + "parent": "Development" |
| 127 | + }, |
| 128 | + { |
| 129 | + "title": "Contributing Guidelines", |
| 130 | + "purpose": "How to contribute code, report issues, and follow project conventions", |
| 131 | + "parent": "Development" |
| 132 | + }, |
| 133 | + { |
| 134 | + "title": "API Reference", |
| 135 | + "purpose": "Auto-generated API docs from Python docstrings for all suite2p subpackages", |
| 136 | + } |
| 137 | + ] |
| 138 | +} |
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