generate_cell_analysis_charts
Generate Cell Analysis Charts
Overview
generate_cell_analysis_charts is the visualization layer of the LabOS cell-video analysis pipeline. It ingests the structured JSON payload produced by analyze_lab_video_cell_behavior (or any schema-compatible source) and renders a curated set of cell-biology-specific figures using matplotlib and seaborn — from population growth curves with 95% CI bands to color-coded single-cell trajectory overlays and 96-well compliance heatmaps — then saves each figure as a print-ready PNG or vector PDF suitable for journal submission, ELN attachment, or real-time XR spatial display.
When to Use This Skill
Use this skill when any of the following conditions are present:
- Downstream of cell video analysis:
analyze_lab_video_cell_behavior(or an equivalent tracking pipeline) has produced a structured JSON result and the next step is to visualize it — without writing ad-hoc plotting code from scratch. - Publication figure preparation: A manuscript or poster requires one or more standard cell biology figures (growth curve, trajectory map, phenotype distribution, MSD plot) at 300 DPI with colorblind-safe palettes and clean axes styling.
- ELN / Benchling figure attachment: A post-experiment summary must include standardized charts appended to a Benchling ELN entry or protocols.io run record.
- Multi-well plate visualization: A high-content screening experiment (96- or 384-well) yielded per-well metrics that need to be rendered as a plate heatmap for quick hit identification.
- Drug dose-response reporting: Per-well doubling times or apoptosis rates from a cytotoxicity experiment need to be plotted on a log-dose axis with a sigmoidal fit and IC50 annotation.
- XR spatial dashboard: Live or post-hoc cell metrics need to be rendered as lightweight PNG panels to embed in an XR overlay above the microscope stage via LabOS.
- Batch multi-experiment comparison: Several JSON files from different conditions, cell lines, or time points need to be overlaid on a single comparison figure with automatic legend and color assignment.
- Report or slide deck generation: Downstream skills (
pptx-generation,scientific-writing,latex-posters) need pre-rendered figure files with predictable filenames and standardized aspect ratios.
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