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Complete guide to preprocessing and analyzing C. elegans embryonic development using spatio-temporal graph data

Data Pipeline & Architecture Documentation System Architecture Diagram ┌─────────────────────────────────────┐ │ C. elegans Embryo Microscopy │ │ (EPIC fluorescence video) │ └──────────────┬──────────────────────┘ │ ↓ ┌─────────────────────────────────────┐ │ Raw EPIC CSV Files (260) │ │ dataset/raw/*.csv │ │ │ │ Columns: │ │ cell, time, x, y, z, size, blot │ │ (+ unused metadata columns) │ │ │ │ Format: N×T sparse table │ │ (only alive cells per timepoint) │ └──────────────┬──────────────────────┘ │ ┌──────────────────────┴──────────────────────┐ │ │ [preprocess_dataset....

EPIC Database Preprocessing & Tensor Conversion Documentation Overview This document describes the complete transformation pipeline that converts raw EPIC (eMbryo Project Imaging Consortium) microscopy CSV files into optimized tensor representations suitable for spatio-temporal graph neural network training. The pipeline produces N×d×T node feature tensors and sparse directional graphs representing both spatial proximity and biological cell lineage relationships, enabling analysis of C. elegans embryonic cell division and migration. 1. Input Data: Raw EPIC CSV Format 1....

EPIC Database Quick Reference One-Liner File Structure Raw EPIC CSV (260 files) ↓ preprocess_dataset.py Processed NPZ (260 per-embryo tensors) ↓ np.load() X[N, d=5, T], alive_mask[N, T], edge_src/dst/t, idx_to_cell[N] Dimensions at a Glance Variable Shape Dtype Meaning X (N, 5, T) float32 Node features: x, y, z, size, blot alive_mask (N, T) bool Cell is alive at time t edge_src (E,) int32 Edge source node edge_dst (E,) int32 Edge destination node edge_t (E,) int32 Edge timepoint idx_to_cell (N,) object Cell name for node index Example (CD011605_5a_bright): N = 688 cells d = 5 features T = 210 timepoints E ≈ 56,605 edges Minimal Working Example import numpy as np # Load npz = np....

EPIC Database Documentation Index Quick Navigation 📖 For First-Time Users Start here: QUICK_REFERENCE.md — 5-minute overview Then read: DATABASE_DOCUMENTATION.md — Sections 1–3 (input, processing, output) Try this: Run python scripts/usage_examples.py to see working code 🏗️ For System Design ARCHITECTURE.md — Data flow diagrams, tensor construction, edge building logic 💻 For Implementation Database_DOCUMENTATION.md — Code recipes and patterns scripts/usage_examples.py — 7 runnable examples src/epic_preprocess.py — Core preprocessing functions 🔍 For Debugging & Validation DATABASE_DOCUMENTATION....

EPIC Database Schema Reference Dataset Specification Project: Spatio-Temporal Evolution (C. elegans EPIC embryos) Format Version: 1.0 Schema Date: April 2026 Overview Raw Data (260 CSV files) ↓ Per-embryo processing ↓ Processed Data (260 NPZ archives) 1. Input Schema: Raw EPIC CSV File Format Location: dataset/raw/*.csv Format: CSV (comma-delimited) Count: 260 files (one per embryo) Encoding: UTF-8 Column Specification Column Type Unit Range Required Used? Notes cellTime string — — ✓ ✗ Row ID (e....