phenopype / phenopype

A phenotyping pipeline for Python

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phenopype

phenopype is a Python package for rapid extraction of phenotypic information from standardized images. It comes with a basic toolset for image preprocessing and signal-processing-based segmentation, but also leverages state of the art AI segmentation models like Fast Segment Anything through a growing set of plugins. Additionally, phenopype includes functionality for visualization of image processing results and export into various file and training data formats (json, csv, coco, ...).

phenopype is aiming to augment, rather than replace the utility of existing computer vision libraries. Put differently, phenopype does not intend to be an exhaustive library of granular image processing functions, like OpenCV, scikit-image or ImageJ, but instead provides a set of wrappers and convenient management tools to allow users to get their data fast without having to fiddle with too much code. As such, phenopype may also serve as a stepping stone for ecologists and evolutionary biologists who are interested in implementing computer vision workflows.

Quickstart

https://www.phenopype.org/docs/quickstart/

Main features

(For a complete list check the API reference)

• image analysis workflow:
  • preprocessing (automatic reference-card and QR-code detection, colour and size correction, morphology operations)
  • segmentation (thresholding, watershed, contour-filtering, foreground-background subtraction)
  • measurement (pixel intensities, landmarks, shape features, texture features)
  • visualization (various options) and export (csv, json, ROI images, ...)
  • video analysis module for object tracking
• project management tools to organize images and data (automatic creation of project directory tree)
• customizable analysis-templates that allow anyone to reproduce all collected data with only a few lines of code (suitable for repositories like Dryad or OSF).

Contributions and feedback

phenopype development is ongoing and contributions towards making it more broadly applicable and user-friendly are more than welcome. This can be done by submitting issues or feature requests in the issue tracker. You can also get in touch with me directly if you would like to contribute.

How to cite phenopype

Lürig, M. D. (2021). phenopype : A phenotyping pipeline for Python. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13771

@ARTICLE{Lurig2022-pb,
  title     = "phenopype : A phenotyping pipeline for Python",
  author    = "L{\"u}rig, Moritz D",
  journal   = "Methods in ecology and evolution / British Ecological Society",
  publisher = "Wiley",
  volume    =  13,
  number    =  3,
  pages     = "569--576",
  month     =  mar,
  year      =  2022,
  copyright = "http://creativecommons.org/licenses/by-nc/4.0/",
  language  = "en",
  issn      = "2041-210X",
  doi       = "10.1111/2041-210x.13771"
}

phenopype's Issues

no able to get images from gallery

Hi Moritz, two things form Project 6.

1. proj = pp.Project("project") should be replace for proj = pp.project("project") in the documentation
2. I have got a problem getting the images for the example.

add the two snail-images from the data folder

proj.add_files(image_dir = r"../../gallery/data", include="snails")

show I get them from the main phenopype repo (I don't find them) or are they in a hidden folder during the installation? because I can't find them

Thanks

yaml-file opening closes comment window before comment has been made.

This triggers if the order of windows opening between the yaml-editor and the image window happens in a certain way.
speifically:

1. image-window with comment opens first
2. yaml-editor opens second. This causes the image window to close and then reopen. If you were about to write a comment, upon reopening the comment is considered done.
   I.e. If edit=false, you are now unable to enter a comment without changing to edit=true in the yaml-file.

I'm running this in a virtual windows environment that is pretty slow. It might not affect users running phenopype natively.

Function missing in release 1.0.5

phenopype/phenopype/core/visualization.py

Line 314 in db01f70

def draw_mask(

Hi everyone,

I just installed phenopype via pip into my virtualenv and wanted to start with your tutortials.
It seems that the function draw_mask is missing in this release. I checked the file "core.visualization.py" in the side package folder of the virtualenv and there was no such function but one called draw_masks which takes slightly different parameters.

It the draw_mask function depricated or is this a bug?

Thanks and cheers,
Sebastian

Trailing "?" added to comments

If image window is closed with alt+enter instead of enter after writing a comment, a trailing "?" is added to the comment