Napari-zelda

"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 <b>2D</b>: '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 <b>3D</b>: 'parent label', 'label' , 'area', 'volume', 'intensity_mean', 'intensity_min', 'intensity_max', 'equivalent_diameter', 'axis_major_length', 'axis_minor_length', 'centroid', 'centroid_weighted', 'extent', 'solidity'

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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

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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

"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.

----------------------------------------------------------------------------------------
Improvements:
- added FilterByArea_widget
- added object labels to result tables

----------------------------------------------------------------------------------------
Fix:
- now compatible with scikit-image 0.21.0

"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.

----------------------------------------------------------------------------------------
Improvements:
- can measure different images using the same labels and save multiple times the results
- implemented Volume calculation

----------------------------------------------------------------------------------------
Fix:
- image calibration

"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.

----------------------------------------------------------------------------------------
Improvements:
- can measure different images using the same labels and save multiple times the results

----------------------------------------------------------------------------------------
Fix:
- scikit-image<=0.18.3

"ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari"
Authors: Rocco D'Antuono, Giuseppina Pisignano
preprint: https://www.biorxiv.org/content/10.1101/2021.10.24.465596v1
example data sets: https://zenodo.org/record/5651284#.YYgn_WDP2Ch

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 "Import and Export Protocols" that allows sharing custom-developed protocols with the bioimage community, in a few clicks.

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Fix:
- parent label handling with "datatable" instead of pandas

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Acknowledgements:
- Ana Stojiljkovic [StojiljkovicVetAna](https://github.com/StojiljkovicVetAna) and Ewelina Bartoszek [ewelinabartoszek](https://github.com/ewelinabartoszek)

"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

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Fix:
- use "datatable" instead of "pandas" to handle results

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Acknowledgements:
- Ana Stojiljkovic [StojiljkovicVetAna](https://github.com/StojiljkovicVetAna) and Ewelina Bartoszek [ewelinabartoszek](https://github.com/ewelinabartoszek)