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ZELDA v0.1.12

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@RoccoDAnt RoccoDAnt released this 10 Aug 21:47
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v0.1.12
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ZELDA v0.1.12

"ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari"

Authors: Rocco D'Antuono, Giuseppina Pisignano

Article: Front. Comput. Sci., 04 January 2022 | https://doi.org/10.3389/fcomp.2021.796117
Examples of 2D and 3D data sets: https://doi.org/10.5281/zenodo.5651284

PROTOCOLS:

"Segment a single object population"

The protocol allows to segment a single object type such as cell nuclei or vesicles.

"Segment two object populations and relate Parent to Child"

The protocol allows to segment in parallel two populations.
The larger objects, called Parents, may contain the smallest ones called "Children".
For example, cytoplasmic organelles can be segmented, labelled, and measured according to the parent cell.

"Data Plotter"

The protocol can be used to plot and save histograms and scatterplots of previously obtained result tables.

"Design a New Protocol"

A custom-made image analysis protocol can be assembled using the available functions, such as Threshold, GaussianBlur, etc.

MEASUREMENTS

  • in 2D: 'parent label', 'label' , 'area', 'intensity_mean', 'intensity_min', 'intensity_max', 'equivalent_diameter', 'axis_major_length', 'axis_minor_length', 'centroid', 'centroid_weighted', 'extent', 'solidity', 'orientation', 'perimeter'
  • in 3D: 'parent label', 'label' , 'area', 'volume', 'intensity_mean', 'intensity_min', 'intensity_max', 'equivalent_diameter', 'axis_major_length', 'axis_minor_length', 'centroid', 'centroid_weighted', 'extent', 'solidity'

Improvements:

  • added the measurements of centroid, weighted centroid, extent, and solidity for 2D and 3D.
  • added the measurements of orientation and perimeter for 2D.
  • added FilterByArea_widget (with v0.1.11)
  • added object labels to result tables (with v0.1.11)
  • removed the use of datatable; pandas is used instead for saving and importing .csv files

Fixes:

  • now compatible with scikit-image 0.21.0 (from v0.1.11)
  • improved the identification of local maxima in 3D with the option exclude_border=False in skimage.feature.peak_local_max
  • excluded from the data plot invalid values such as np.inf, np.NINF, and the use of drop.na
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