Menu Curate
The MorphoNet standalone application allows to curate 3D+t segmented datasets. This is done on local datasets, on temporary data, so your original images are unchanged. Upon dataset export, you can export your curated images.
The concept is based on a duality between the segmented image and the construction of 3D mesh objects for each individual label. While the meshes object are extremely powerful for 3D visualization and interaction, the 3D segmented image remains the desired output. The curation is performed in 4 steps:
- Users identify their issues to curate using the viewer based on the interaction with the messages (using the lineage window, the intensity Images, the properties...)
- Users find and launch the most appropriate plugin to solve their issue
- The plugin performs the curation and actions directly on the segmented image
- MorphoNet automatically recomputes the updated meshes from the segmented image, modified by the plugin and updates the visualization.
IMPORTANT ! Labeled vs Selected
When a selected object is required to run the plugin, it can be either a selected object (at a given time point) (Figure a) or labeled object (which can be used at different time points) (Figure b).
Unless specified, all plugins that require selected objects will run on selected and labeled objects. Before launcing a plugin, be careful if you have labeled objects on which you do not want to apply a plugin.
The plugin control panel on the right shows a preview of the objects on which plugins will be applied, and allows to choose whether or not to run plugins on selected objects and/or labeled objects.
This menu will be explained in better detail below.
Curation Menu
The curation menu contains in the left menu with tools, and on the middle a list of available plugins.
On the Right, there are the plugin control panel and the menus of the currently selected plugin, if there is oneTo select a plugin, just click on its icon. Selecting a plugin will open its description, its parameter panel (if it has parameters), and will update the plugin control panel.
Hovering over a plugin button for a second will also show its description and parameter panel while hovered. Below, the Binarize plugin has been selected as an example.
Plugin control panel
Just above the selected plugin description, and parameters there is the plugin control panel.
It allows to review on which elements of your dataset the selected plugin will run, and to add or exclude elements. The big Play button in the bottom right runs the selected plugin.
IMPORTANT NOTICE: Most plugins run only on selected and/or labeled objects. But some also run on whole images (whole time points and channels), and some run exclusively on images.
If the plugin runs on images, it will show the times and channels on which it runs in the final summary.
If it runs on selected/labeled objects it will tell you the object count. If the plugin runs exclusively on images it will show this regardless you have selected objects or not.| Buttons | Functions |
|---|---|
| Times | Allows you to select or exclude time points on which to run the plugin. If a plugin runs on selected/labeled objects, any selected or labeled object outside of the selected time(s) will be ignored, and is not shown in the final count. |
| Channels | Allows you to select or exclude channels on which to run the plugin. If a plugin runs on selected/labeled objects, any selected or labeled object outside of the selected channel(s) will be ignored, and is not shown in the final count. |
| Selected objects | Choose whether plugins will run on selected objects or not. Will update the final summary count |
| Labeled objects | Choose whether plugins will run on labled objects or not. Will update the final summary count |
| Final summary | Summary of what the plugin will be running on. In the above example, no objects are selected or labeled, so the plugin will not run. |
Tools menu
The tools menu contains a list of buttons that do the following:
| Buttons | Functions |
|---|---|
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Navigate steps: Use the left and right arrow to go to the previous and next step respectively. The red cross allows yo to cancel to the current step (current step included). |
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Highlight cells and navigate potential issues: The left button allows to highlight the selected cell(s). It is the same as maintaining the 'H' key pressed. The left and right arrow are active if your dataset has a lineage property. it navigates to the next or previous potential error (cell death, cell bith and division) in lineage. |
 |
Seeds: The leftmost button toggles the seeds visualization. It will allow you to see the seeds cursor (which may be hidden at the center of the dataset by default). Move it by maintaining the 'T' key pressed and by moving the mouse. The middle button adds a seed on the position of the cursor. The rightmost button deletes all seeds. |
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Copy-paste menu: The leftmost button activates the copy-paste menu. It is used for the Copy-Paste plugin. The middle button copies the currently selected object. you will notice a wireframe effect on the mesh. The rightmost button deletes all copied cells. |
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Mesh morphing menu: The leftmost button activates the mesh morphing menu. It is used for the mesh morphing plugin. It requires that you selected an object beforehand of activating it. See below for the full mesh morphing and what is does. The left and right arrows allow you to undo/redo mesh morphing operations you have done on the currently morphed mesh. |
Mesh deformation menu
The Deform plugin contains a specifc menu accessible from the tools menu. In order to deform a mesh, it must be selected before opening the deform menu.
Each of the 4 symbols on his top correspond to a different method of mesh deformation. Each deformation method has a radius of influence, that can be changed with the slider.
From Left to right :
- Smooth : smoothes the overall shape of the mesh around the cursor. The smoothing tends to slightly “deflate” the mesh
- Sculpt : elevates the mesh around the cursor.
- Carve : hollows the mesh around the cursor.
- Grab : grab a part of the mesh and move it around.
The two arrow buttons allow you to revert and re-apply deformations.
Plugins Menu
On mouse over each plugin icons, you will have a description of the plugin
If you click on a specific icons you will get the list of accessible parameters and the possibility to launch the plugin.
Short cuts
- 'A' for Add a seed
- 'C' for remove last seed
- 'D' to delete the seed pointed by the mouse