BactoScoop

Single-cell measurements from multichannel bacterial microscopy

I developed BactoScoop to connect bacterial cell morphology with measurements from multiple fluorescence channels. The workflow starts with microscopy images and labeled cell masks, reconstructs a coordinate system for each cell, and extracts measurements into a per-cell table after geometry review and curation.

Follow the guides to run that workflow, inspect intermediate results, and understand the measurements before using them in an analysis. Start with Installation and Quick start, or follow the Three-channel walkthrough: DAPI and GFP-DnaN objects and Five-channel walkthrough: membranes and multichannel profiles tutorials.

BactoScoop logo
Images→Masks→Meshes→Curation→Objects & signals→Feature tables

What BactoScoop measures

  • Cell morphology: length, width, projected area, estimated volume, curvature, constriction, and region properties.

  • Signal profiles: axial and mesh-based intensities, radial distributions, normalized profiles, and texture descriptors.

  • Detected objects: counts, projected geometry, positions relative to the cell axis and poles, intensities, and estimates based on valid object meshes.

  • Membrane-associated signals: contour profiles, gradients, and texture.

  • Relationships between channels: implemented correlation and similarity measurements applied to matching feature values or profiles.

These measurements describe the supplied images and reconstructed geometry. Biological conclusions require experimental controls and an appropriate analysis of the resulting tables. BactoScoop’s current image workflow is 2D; volume is estimated from a 2D mesh, rather than measured from a 3D acquisition.

Two ways to learn

The three-channel example uses phase contrast, DAPI, and GFP-DnaN to inspect intracellular objects. The five-channel example adds outer- and inner-membrane signals and RNA measurements. Both tutorials include real figures saved in the repository’s notebooks, complete code, and explanations of the intermediate steps.

This guide covers BactoScoop 0.1.2. Start with the installation guide and a walkthrough, then explore the analysis workflow and API reference.

Getting started

Analysis workflow

Examples

Reference