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 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”). |
Image source: К562_(Light_microscopy), Creative Commons Attribution-Share Alike 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/deed.en) |
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 References¶
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
Multiple birth and cut algorithm for multiple object detection; Gamal Eldin, Descombes, Charpiat, Zerubia; JMPT (ISSN: 0976-4127, ESSN: 0976-4135); 2012
DOI: 10.1.1.661.9041
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
- using
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
- using the core module
For Customizers = Library hackers willing to:
- modify
mpp.py
- add new object type and object quality definitions
- modify
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: