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 :doc:`getting-started/installation` and :doc:`getting-started/quickstart`,
or follow the :doc:`examples/three-channel` and :doc:`examples/five-channel` tutorials.

.. image:: _static/logo.png
   :alt: BactoScoop logo
   :width: 280px
   :align: center

.. raw:: html

   <div class="workflow" aria-label="Analysis workflow">
   <span>Images</span><b>→</b><span>Masks</span><b>→</b><span>Meshes</span><b>→</b><span>Curation</span><b>→</b><span>Objects &amp; signals</span><b>→</b><span>Feature tables</span>
   </div>

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.

.. toctree::
   :caption: Getting started
   :maxdepth: 1

   getting-started/installation
   getting-started/gpu
   getting-started/quickstart
   getting-started/inputs
   getting-started/outputs

.. toctree::
   :caption: Analysis workflow
   :maxdepth: 1

   workflow/segmentation
   workflow/meshes
   workflow/curation
   workflow/alignment
   workflow/objects
   workflow/features
   workflow/correlation
   workflow/export
   workflow/errors

.. toctree::
   :caption: Examples
   :maxdepth: 1

   examples/three-channel
   examples/five-channel
   examples/reuse
   examples/plotting
   examples/parallel

.. toctree::
   :caption: Reference
   :maxdepth: 1

   reference/feature-dictionary
   reference/parameters
   api/index
   reference/data-structures
   reference/troubleshooting
   reference/project