Releases: RoccoDAnt/napari-zelda
ZELDA v0.1.12
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
ZELDA v0.1.11
"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 v0.1.10
"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 v0.1.9
"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 v0.1.7
"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.
Fix:
- parent label handling with "datatable" instead of pandas
Acknowledgements:
- Ana Stojiljkovic StojiljkovicVetAna and Ewelina Bartoszek ewelinabartoszek
ZELDA v0.1.5
"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:
- Ana Stojiljkovic StojiljkovicVetAna and Ewelina Bartoszek ewelinabartoszek
ZELDA v0.1.4
"ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari"
Authors: Rocco D'Antuono, Giuseppina Pisignano
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.
Improvement: layers opened before launching the plugin are listed in the widgets
Fix: protocol management os-agnostic (win, mac)
Acknowledgements:
Peter Carlton pmcarlton
ZELDA v0.1.3
"ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari"
Authors: Rocco D'Antuono, Giuseppina Pisignano
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.