Obj.MPP: Object/pattern detection using a Marked Point Process

This documentation describes the usage of the Obj.MPP tools whose source code is available on a GitLab repository.

What does Obj.MPP do?

In Images

Looking for disk-like objects (other shapes available):

image result
Image with a region of interest (ROI) identified by the green rectangle. Disk-like objects found by Obj.MPP inside the ROI (“inside” in the sense “disk center is inside”).

In a Few Words

Obj.MPP implements the detection of parametric objects (or patterns) in a signal based on a quality measure using a Marked Point Process (MPP).

  • Detecting an object in a signal amounts to finding a position p (a point) paired with a set of parameters m (called marks here [1]), the quality measure of which being above some threshold.
  • The detection task amounts to finding all such objects in the signal.
Parametric object
An n-dimensional region defined by a finite set of parameters, typically real numbers. For example, a disk (n=2, position=center, mark(s)=radius). See Standard Object Types.
Signal
A mapping between an n-dimensional position and a d-dimensional vector. For example, a 2-dimensional grayscale image (n=2, d=1).
Quality measure
A way to compute a real number measuring how well a given parametric object fits the signal at a given position. For example, object brightness compared to the surrounding area (i.e., object contrast). See Standard Quality Measures.

Footnotes

[1]Hence the “marked point” terminology.

Bibliographic Reference

Detecting and quantifying stress granules in tissues of multicellular organisms with the Obj.MPP analysis tool; de Graeve, Debreuve, Rahmoun, Ecsedi, Bahri, Hubstenberger, Descombes, Besse; Traffic (Wiley, ISSN: 1398-9219, ESSN: 1600-0854); 20(9), 697-711, 2019

DOI: 10.1111/tra.12678

Citation: BibTeX and EndNote

Installation

Follow the instructions on the Installation and Requirements page.

Documentation Sections

  • For Users = Software users willing to:

    • detect objects…

      • using mpp_detector_cli.py (command line interface)
      • or mpp_detector_gi.py (graphical interface)
      • and the provided object type and object quality definitions
  • For Developers = Library users willing to:

    • add the Obj.MPP object detection capability in some piece of software…

      • using the core module mpp.py
      • and the provided object type and object quality definitions
  • For Customizers = Library hackers willing to:

    • modify mpp.py
    • add new object type and object quality definitions
  • For Reviewers = Code checkers willing to:

    • understand the structure of Obj.MPP
    • hunt for bugs
    • imagine structure, code readability, code conventions, code conformity, performance improvements

Typical browsing route for users:

  1. Obj.MPP for Users
  2. Using mpp_detector_cli.py
  3. Configuration File
  4. Generic Configurations
  5. Standard Object Types
  6. Standard Quality Measures.