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

Choose a Protocol from the drop-down menu below and click "Run".

PROTOCOLS
- "Segment a single object population".
The protocol allows to segment a single object type such as cell nuclei or vesicles
Suggested steps:
1. Image calibration
2. Gaussian Blur
3. Threshold
4. Distance map
5. Show seeds
6. Watershed
7. Measure objects
8. Plot data and save graphs.

- "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.
Suggested steps:
1. Image calibration
2. Gaussian Blur
3. Threshold
4. Distance map
5. Show seeds
6. Watershed
7. Relate and Measure objects
8. Plot data and save graphs

- "Data Plotter".
The protocol can be used to plot and save histograms and scatterplots of previously obtained result tables.
1. Load a result table
2. Use the Histogram/Scatter tool to explore the data
3. Save the plots

- "Design a New Protocol".
A custom-made image analysis protocol can be assembled using the available functions, such as Threshold, GaussianBlur et cetera.
1. Choose a name for the new protocol
2. Set the number of steps for the new protocol
3. Click "Design"
4. Assign a function to execute at each step
5. Save the new protocol
The new protocol will be available in the drop-down menu after restarting napari.

- "Import and Export Protocols".
Custom protocols can be imported/exported and exchanged with the community in few clicks.
1. Choose a .json file containing the current protocols.
2. Choose a destination .json file
3. Protocols will be appended to the existing destination file, or a new file will be created.
4. You new .json file will contain your protocols, so they can be exchanged with the community.
