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Vision 4D 3.2
Application Note #9
How to perform :
«the Compartmentalization’ analysis»
The application-note purpose is to guide the user in performing a
Compartmentalization analysis. It explains how to setup a study
focused on the interactions and of the relationships between
compartments of the structure under evaluation.
“The quantitative analysis of the images represents the art of transforming a
visual sensation into its schematic and discrete form allowing its univocal
description, classification and mathematical and logical interpretation of its
spatial and temporal components”
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Application Note
«Compartmentalization analysis»
Vision4D 3.2 2
Application Flowchart
•The reference (Parent) segments can be created in
the same pipeline on which the task is performed,
or imported from the data table
Detect or import the reference objects
•The subject (Child) segments can be created in the
same pipeline on which the task is performed, or
imported from the data table
Detect or import the subject objects
•Perform the Compartmentalization’ analysis
Compartmentalize
Index
1. Overview.
2. The Compartments Operator.
3. Single Compartments (2 levels).
4. Single Compartments (multiple levels).
5. Multiple Compartments (multiple levels).
6. Compartments example
7. Special Application
8. Tips
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Application Note
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1. Overview
The COMPARTMENTALIZATION’ concept is strictly related to
the studies of the interactions and of the relationship between
the structure' compartments.
Complex hierarchies between the structures can be established
and evaluated using this operator. Objects inside a parent
structure can be selected, their position inside the main
structure, as well as their distribution (clustering), and other
features, can be evaluated. A child object can be a parent for
other objects. The number of the available nested levels are,
theoretically, unlimited.
Main level
(Parent)
E.G. Cells
Second level
(Children)
E.G. Nuclei
Third level
(Children of Children)
E.G. Vesicles
In the example here above, The COMPARTMENTALIZATION is
extended on 3 levels. The result is a hierarchical link between
the Cell (Reference) and its nucleus (subject) . The nucleus is, in
turn, related to the vesicles it contains. Finally, the vesicles
count per cell is obtained.
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1. Overview (continue)
The COMPARTMENTALIZATION’ analysis is not limited to the
biological samples, even if this is the most common situation.
Any structure located inside of a defined surrounding volume
can be evaluated.
It is not mandatory that the parent object is a defined
structure (E.G. Cell or Nucleus), it can be an anatomical region
or, generally speaking, a sub-region of interest of the sample
volume.
These regions can be drawn both manually or using the
interactive method.
NOTE :
Refer to the Application Note #8 for detailed information about «How
to Draw objects interactively»
The COMPARTMENTALIZATION’ approach is the base on which
more complex and sophisticated evaluations can be
performed.
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Application Note
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2. The Compartments Operator
2.1 The Compartments Operator allows to set the structures
hierarchy to be used to evaluate their levels of relationships.
Several nested levels are possible as well as two or more
compartments at the same hierarchical basis.
2.2 Settings for Compartments:
• Add the TAG of the structures of interest as a
source entry.
• Use the input selection button to select a
different operation from the preceding pipeline.
• Remove the selected TAG from the entry.
• Move the selected TAG up & down in the
hierarchical levels.
• Move the selected TAG as a "child" of the
“parent” above it and push it up or down in the
hierarchy.
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Application Note
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2. The Compartments Operator (continue)
• Select the required amount of overlap.
1. Partial Overlap.
Check whether a "child" segment is
partially covered by a "parent"
structure. You can set the necessary
amount of overlap with the slider or
the text input.
2. Full Overlap.
Check whether a "child" structure is
fully covered by a “Parent" volume.
NOTE :
The Partial Overlap defined the percentage of the subject structure
volume that must be covered by the Reference volume to be considered
as compartmentalzed.
If you choose 0%, it still checks whether there is at least 1 voxel of
coverage.
COMMENT :
The selected parent TAG, as well as the child TAG can label more objects.
For any object in the Parent TAG, all the child objects are compared to it in order to
establish their belonging.
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Application Note
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3. Simple Compartments (2 levels)
3.1 The Simple Compartments' schema is organized on two
levels of hierarchy, the Reference (Parent) and the Subject
(Child). The child objects belonging to the Parent spaces are
labelled (TAG) as compartmentalized.
Segment Generation
(Reference)
Segment Generation
(Subject)
Compartments
• Reference
• Subject
NOTE :
These Reference structure can also be drawn both manually or using the interactive
method. Refer to the Application Note #8 for detailed information about «How to
Draw objects interactively»
The left most item is a reference
The items below the left most
item is the subject. It must be
shifted one position on right
compared to the reference.
TIPS :
The commands on top of the dialog
are used to set the hierarchy. (refer
to Page 6)
Compartments setup:
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4. Multiple Compartments (multiple levels).
4.1 The Multiple Compartments’ schema uses 3 levels or more
of hierarchy. Starting from the first child on the top, each of
the level is checked with the previous one. The child objects
belonging to its Parent spaces are labelled (TAG) as
compartmentalized.
Segment Gener.
(Reference)
Segment Gener.
(Subject)
Compartments
• Reference
• Subject
• Subject
Segment Gener.
(Subject)
The left most item is a reference
The items below the left most
item is the subject. It must be
shifted one position on right
compared to the reference.
The 3rd levels is set shifting the
TAG one position on right
compared to the subject on top
of it.
Compartments setup:
TIPS :
The commands on top of the dialog are used to set the hierarchy. (refer to Page 6)
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Application Note
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5. Single Compartments (multiple subjects).
5.1 The Simple Compartments' schema (multiple subjects) is
organized on two levels of hierarchy, but the child level can
have more entries. The child objects of each entry, belonging
to the Parent spaces, are labelled (TAG) as compartmentalized.
Segment Gener.
(Reference)
Segment Gener.
(Subject)
Compartments
• Reference
• Subject
• Subject
Segment Gener.
(Subject)
Compartments setup:
The left most item is a reference
The items below the left most
item is the subject. It must be
shifted one position on right
compared to the reference.
The 2nd subject is set to the
same level of the
NOTE :
The Compartments results are shown in the data table. The TAG «Compartments» is
used to label the classified objects.
TIPS :
The commands on top of the dialog are used to set the hierarchy. (refer to Page 6)
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Application Note
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6. Compartments example
Reference Subject Result
6.1 Simple Compartments (2 levels)
6.2 Multiple Compartments (multiple levels).
Reference Subject #1 Subject #2 Result
6.3 Single Compartments (multiple subjects).
Reference
Subject #1 Subject #2 Result
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7. Special Compartments application
7.1 Objects density distribution (heat-map).
The purpose of the density distribution task, is to evaluate,
through a colored map (heat-map), the objects population
concentration per volume’ unit inside the whole sample.
Contiguous, regularly sized, boxes are created to divide the
whole volume sample in sub spaces.
These boxes are used as Parent to establish the
compartmentalization of the counted objects (child) in the
sampled volume. The different colors shows the density (or
concentration) in the specific sub space. Usually, the cold
colors (E.G. Blue hues) show a low concentration while the hot
colors (E.G. red hues) show high concentration values.
Objects count per sub volume
TIPS :
A Python script (Divide Scope) is
available to create the sub-volumes
boxes matrix (Parent objects).
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7.2 Object gradient profile.
The Object gradient profile task, computes the concentration’
gradient of the child objects along a specific direction.
Regular sized boxes are created to cover the selected part of
the volume' sample with contiguous subspaces.
These boxes are used as Parent to establish the
compartmentalization of the counted objects (child) in the
sampled volume. The boxes can be created following a linear
progression, or covering a more complex paths (E.G. Spiral
path)
7. Special Compartments application (continue)
1
10
1
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8.4 A Python scripts (Segments rotation, Spiral Oriented Sub
Volume) are available to create the sub-volumes boxes matrix
(Parent objects) described in the chapter 7.
8. Tips
8.1 The Application Note #1 (Gradient) describes the steps to
achieve the linear gradient' profile (objects count along a
specific path), as well as the map of the concentrations ("Heat
Map" - objects count per volume unit).
8.2 The Application Note #6 (Spiral Oriented Sub Volume)
describes the steps to achieve the spiral gradient' profile
(objects count along a specific concentric path) .
8.3 The Application Note #8 (Draw Manual Objects) describes
the steps to draw objects interactively.
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arivis AG . Imaging Science .
Erika-Mann-Straße 23 . Munich
Email : support@arivis.com
Contact the arivis local area sales manager to get more
information about how to get the python scripts mentioned
here.
Contact the arivis application support to receive additional
technical details about the topic described in the application
note, or how to adapt the application workflow to your
requirements.
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