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ZELDA v0.1.5
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@RoccoDAnt RoccoDAnt released this 05 Nov 23:52
· 49 commits to main since this release
v0.1.5
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"ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari"

Authors: Rocco D'Antuono, Giuseppina Pisignano

https://www.biorxiv.org/content/10.1101/2021.10.24.465596v1

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.

Improvements:

  • introduced Otsu threshold option.
  • introduced image calibration step to set voxel size (pixel and z interval).
  • added new measurements. Available in the current release: 'area', 'mean_intensity', 'min_intensity', 'max_intensity', 'equivalent_diameter', 'major_axis_length', 'minor_axis_length',' feret_diameter_max', Parent label

Fix:

  • use "datatable" instead of "pandas" to handle results

Acknowledgements:

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