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Add support for different colony morphology #38

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Erik-White opened this issue Jan 29, 2020 · 0 comments
Open

Add support for different colony morphology #38

Erik-White opened this issue Jan 29, 2020 · 0 comments
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enhancement New feature or request
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0.6.0

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@Erik-White
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Erik-White commented Jan 29, 2020 •
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Currently the package is able to identify circular, even colonies. This is adequate for most use cases, however extending support to colonies with other morphologies would allow study of a wider range of species and conditions.

With different colony types it would be useful to drawn comparison between the different types:

  • The relative ratios of the colony morphologies present
  • The relative intensities of the colonies
  • The ratio of total colony area to background

Example morphologies
@Erik-White Erik-White added the enhancement New feature or request label Jan 29, 2020
@Erik-White Erik-White added this to the 0.5.0 milestone Jan 29, 2020
Erik-White added a commit that referenced this issue Feb 8, 2020
@Erik-White
Increase the flexibility and modularity of the package. Implement bas…
ec0c59c 
…e classes (#35)

Increase the flexibility and modularity of the package and reduce the need to manipulate collections of primitives. Provide the basis for being able to implement different types of plate and colony analysis (see #38).

- Adds base classes to provide core functionality
- Create a Plate class (and collection) to store information related to plates and hold a collection of Colony class instances
- Create an ImageFile class (and collection) to store image file paths and timestamp information
- Refactored most of the functions from `main` as static methods in the `plate` or `image_file` modules

- Adds a command line argument, `plate_labels`, to allow labels to be attached to specific plates
- Rename `save_plots` CLA to `plots`

Closes #30
Closes #36
Erik-White added a commit that referenced this issue Apr 12, 2020
@Erik-White
Improve colony segmentation (#44)
7827d54 
* Individual plots for each plate are now output by default
* `plate_size` now defaults to 90 mm, the visible size of a 100 mm plate in a plate holder
* `plate_edge_cut` is now a percentage of the plate diameter, instead of a fixed pixel value
* Improved colony segmentation in low contrast images and under poor growth conditions
* Grouping of colony Timepoints is now faster and more accurate
* Colonies are no longer identified based on circularity. Lays the groundwork for classifying colonies by morphology (see #38)
* Catch outliers and division by zero when calculating growth curves
* Do not occupy all available cores with multiprocessing, leave one free
@Erik-White Erik-White modified the milestones: 0.5.0, 0.6.0 Sep 8, 2020
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