This guide explains you how to perform an interactive objects drawing.
The interactive objects drawing method allows to directly define the structure edges by using one of the many graphic tools available. The object drawing is, not always but often, the unique approach available to get the object outline and shape. This is more evident when the images have a complex texture or a not well defined edges (e.g. EM or CT images).
Vision4D offers a wide drawing tool collection, comprising the fully manual methods as well as some semi-automatic approaches. The drawing tool collection is available on the top icon panel. It's content varies according to the viewing method setting.
With the 4D viewing method on, both the Magic Wand tool as well as the tool to place simple geometric shapes, markers or spheres on the volume are available. The 2D viewing method allows access to more tools, including the Manual Drawing tool, the Magic Wand tool, and the simple geometric shapes creator tool. In this modality, the drawn objects can be also edited.
The objects created manually are, to all purposes, evaluable segments, exactly as the objects gathered using the automatic approach (Pipeline). All the available measurements can be quantified.
These objects can also be applied as free shape ROI to mask part of the volume or managed to perform evaluations about between structures' interactions and relationships (Objects Compartmentalization, Objects Co-Localization, etc.).
To draw objects in 2D, select the 2D view.
The Draw Objects tool is useful to identify complex 3D structures that can’t easily be segmented using threshold-based techniques. This tool can be used to define completely new objects. The objects drawing workflow starts by defining the outline of objects on a 2D plane. The drawing procedure is continued over all the planes on which the object is extending, scrolling through the stack as needed, until the object is completely outlined. Existing objects can be also be modified adjusting the outline shape.
Defining the outline of objects on a 2D plane:
As mentioned previously, rather than to define a new object, the Draw Objects tool can also be used to correct existing objects. In that case you should start by using the Select Object button to first activate an object for editing and then use the brush and erase tools as described above. Users can also use an ellipse of polygon to define the outline on the active plane. In either case the brush or erase tools can still be used to further amend the outline if needed.
The Move Objects tool is used to change the object position. Once the objects have been created, they can be copied or moved in other positions, planes or time points.
Moving an object:
In the presence of a 3D object, the whole segment (shape and volume) will be repositioned.
The Magic Wand tool is the starting point for object editing or identifying a handful of significant objects from a larger selection of objects with similar object features. While all the manual object drawing tools are driven by the pure skill of the user, some objects can be identified more quickly using the Magic Wand tool. Only its visual interpretation defines the size and shape of the object.
The tolerance sets the intensity percentage range that is located around the focused pixel accordingly to the following settings (the selection is added to the object):
This means that in the case of a user looking for bright objects with a tolerance of 50, if the user were to click with a pixel with an intensity of 128, the object would include all pixels within the region with an intensity of 78 or more.
The magic wand can be set up to work on all channels of a multichannel image, or on individual channels as needed by using the Channel Visibility panel.
The Measure tool is a quick and easy way to measure simple distances or areas. It is a way to estimate the size of a structure when required. For example several automatic operators require information concerning the dimension of the structures. Use the Measure Tool to get these informations.
All the objects drawn manually are listed in the data table. Please refer to the Object Table chapter for more details about the data management.
The objects manually created are labelled using a TAG. By default, the TAG inherits the tool name (e.g., the Magic Wand tool has the Magic Wand TAG).
The TAG is an object property assigned to it by the running operator (only the preprocessing operators don't use the TAGs) and used to link all the detected objects to a common collection. By default, the TAG inherits the name from the operator that has generated it. For example, the objects created by BLOB FINDER will have a TAG called “Blob Finder”. The TAG is the Vision4D's way to create a logical and hierarchical relationship between the objects without duplicating them. A single object can belong to many collections. Therefore, it can have numerous TAG's attached to it. The rule is: one object, many TAGs.
The operator's name can be edited. We strongly suggest to rename the operators according to the structure detected typology (e.g., DAPI Nuclei, GFP Cells, etc.).