Cell Analysis Guide¶
This comprehensive guide covers all aspects of automated cell analysis in napari-mAIcrobe, from basic morphometry to cell classification.
π― Overview¶
The "Compute cells" widget provides:
- Morphological analysis β Shape and size measurements
- Intensity analysis β Fluorescence quantification
- Cell classification β Deep learning classification with default models for cell cycle phase determination in S. aureus
- Colocalization analysis β Multi-channel correlation
- Report generation β HTML output
π§ͺ Analysis Workflow¶
Step 1: Prepare Your Data - Segmented cells (Labels layer) - Image channels: membrane and DNA as needed
Step 2: Configure Analysis Parameters
Essential Settings - Label Image: segmentation (required) - Membrane Image: fluorescence channel - DNA Image: DNA staining (optional) - Pixel size: ΞΌm/pixel (optional)
Subcellular Segmentation - Inner mask thickness (default: 4) - Find septum / Find open septum - Septum algorithm: Isodata or Box
Fluorescence Analysis - Baseline margin (default: 30)
Cell Cycle Classification - Enable classification; select model or custom path - Custom model input: Membrane, DNA, or Membrane+DNA - Custom model max size (default: 50 px)
Options - Compute Colocalization - Generate Report (+ Report path) - Compute Heatmap
π Morphological Measurements¶
napari-mAIcrobe computes shape and size parameters using scikit-image regionprops.
Basic Shape Parameters - Area (px, ΞΌmΒ² with pixel size) - Perimeter - Eccentricity
π‘ Intensity Analysis¶
Quantify fluorescence signals in subcellular compartments.
Channel Measurements - Baseline intensity (subtracted from other measures) - Cell Median - Membrane Median - Cytoplasm Median - Septum Median (if detected) - Fluorescence Ratios (100%, 75%, 25%, 10%) when septum enabled - DNA Ratio if DNA channel provided
π§ Cell Classification¶
Use deep learning models to automatically classify cells.
Pre-trained Models - 6 specialized models for S. aureus: DNA+Membrane (Epi/SIM), DNA (Epi/SIM), Membrane (Epi/SIM)
π Colocalization Analysis¶
Quantify spatial relationships between two fluorescence channels using Pearson correlation for Whole Cell, Membrane, Cytoplasm, and Septum (if available).
π Interactive Filtering¶
Use the "Filter cells" widget for real-time quality control: 1. Select Labels layer 2. Add filters for any measured feature 3. Preview filtered population 4. New "Filtered cells" layer contains only the selected cells
π Reports¶
Enable Generate Report to create an HTML report with per-cell images and a CSV with all properties.
Further reading: Cell Classification Guide, API Reference, Tutorials.