Menu Curate
The MorphoNet standalone application allows users to perform the 3D images curation using a new paradigm. This process is done locally on your own dataset without transfering any data to the MorphoNet server.
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 most standard data type for images labels. The curation is performed in 4 steps: * Users identify their issues to curate using the viewer based on the interaction with the messages (using Lineage or Intensity Images) * Users identify and launch the most appropriate plugin to solve their issue * The plugin perform the curation directly inside the segmented image * MorphoNet automatically recompute the modification of the meshes of the labeled which have been modify by the plugin and finally refresh the window
3D image processing such as 3D watershed propagation on large images is usually very slow. We speed up the process by working within the bounding box enclosing each object to be modified rather than on the entire image, thereby giving user feedback within seconds.
Each plugin performs a modification of the 3D segmented images. The modification is done locally on the backup of the segmented images stored inside the MorphoNet application, not on your original data. In order to get the result of your curation, you have at the end the possibility to export your curated segmented images.
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 whiwh you do not want to apply a plugin.
Curation Menu
The curation menu contains in his left part a tools menu and on the right a list of available plugins.
Sidebar
The side 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. |
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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