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trinade edited this page Jul 31, 2025 · 5 revisions

Welcome to the PyPlaque wiki!

Here we provide links to our 4 main modules that have under them relevant classes and subsequent methods and functions. The modules are the following:

  1. The Experiment module which can be viewed as a logical container for several Petri dishes or multi-titre plates united by a similar experimental purpose. For example, an Experiment could be a virus titre determination performed in three biological replicas, which would combine three dishes into one OOP object. This contains classes to handle data and metadata from fluorescence and crystal violet microscopy.

  2. The Specimen module in continuation of the above example could constitute an individual dish/well or biological replicate. This contains classes to handle data and metadata of grayscale or RGB images, binary mask of plaques or plaque-like objects in a single well.

  3. Following the same example, the Phenotype module encompasses, what one may expect to find within this dish, i.e. several plaques - Phenotypes in our abstraction. This contains classes that hold data and metadata of a grayscale image, binary mask of a plaque or plaque like object obtained from fluorescence or crystal violet microscopy.

  4. And lastly, the View module which in our design aims to contain any kind of OOP class aimed for analysis or visualisation obtained from the classes in the three modules mentioned above. The choice of the class to be used in order to construct a specific View defines the granularity of the results. For e.g., if the View is constructed for the granularity of the Phenotype, it would contain measurements of an individual plaque. Whereas if a View is constructed for the entire Experiment it would contain average measurements of plaques in this experiment. Once the classes are instantiated, this information is stored as nested dictionaries. This contains classes that have functions to return tables of generated readouts at the well and plaque level. It also contains a class that given a binary mask to a corresponding plate image can extract image and binary mask pairs of individual wells and also attached positional identifiers to them.

Class under each of the above modules

Experiment

  1. CrystalViolet - This class is designed to contain metadata of multiple instances of a multititre plate of Crystal Violet plaques.
  2. FluorescenceMicroscopy - This class is designed to contain metadata of multiple instances of a multititre plate of Fluorescence plaques.

Specimen

  1. PlaquesImageGray - This class is designed to hold grayscale image data containing multiple plaque phenotypes with a respective binary mask. The class inherits from PlaquesMask.
  2. PlaquesImageRGB - The class is designed to hold RGB image data containing multiple plaque phenotypes with a respective binary mask. The class inherits from PlaquesMask.
  3. PlaquesMask - This class is designed to hold a binary mask of multiple plaque instances in a well.
  4. PlaquesWell - This class is designed to contain a full well of a multititre plate

Phenotypes

  1. CrystalVioletPlaque - This class contains a plaque obtained from crystal violet image. Class inherits from Plaque class and is also designed to hold a single virological plaque phenotype.
  2. FluorescencePlaque - This class contains a plaque obtained from fluorescence image. Class inherits from Plaque class and is also designed to hold a single virological plaque phenotype.
  3. Plaque - This class is designed to hold a single virological plaque phenotype as an object. It encapsulates the properties and behaviors related to a specific plaque, including its mask, centroid coordinates, bounding box, and usage preference for pick measurements.

View

  1. WellImageReadout - This class encapsulates metadata related to multiple instances of plaques within a single well of a fluorescence plate.
  2. PlaqueObjectReadout - This class encapsulate data related to a single instance of a plaque from a fluorescence plaque well.
  3. PlateReadout - This class contains readouts of multiple wells of a single plate of a Fluorescence Plaque.
  4. PlateImage - This class encapsulates a full multi-title plate image and its corresponding binary mask. It provides methods to extract individual well images from the plate based on specified criteria, visualize these wells annotated with their positions, and more.

For more information about class attributes and class functions please refer to the links within each module link.

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