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Copy file name to clipboardExpand all lines: _pages/plugins/snt/delineations.md
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@@ -100,15 +100,15 @@ To re-define a delineation it is sufficient to re-define or re-adjust an existin
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## Hierarchical Labels and Level-split Analysis
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Delineation names support hierarchical labeling using the `::` separator. For example, naming three delineations `Cortex::L1`, `Cortex::L2/3`, and `Cortex::L5` encodes both the parent region (Cortex) and the individual layers. This convention is particularly useful for atlas-imported delineations, where compartments are naturally hierarchical.
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Delineation names support hierarchical labeling using the `:` separator. For example, naming three delineations `Cortex:L1`, `Cortex:L2/3`, and `Cortex:L5` encodes both the parent region (Cortex) and the individual layers. This convention is particularly useful for atlas-imported delineations, where compartments are naturally hierarchical.
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When hierarchical labels are present, the _Measure_ and _Plot_ commands prompt for a **grouping level** before running the analysis. This allows measurements to be aggregated at different levels of granularity without redefining the delineations themselves. For example, with delineations named `Cortex::L1::proximal`, `Cortex::L1::distal`, and `Cortex::L2/3`:
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When hierarchical labels are present, the _Measure_ and _Plot_ commands prompt for a **grouping level** before running the analysis. This allows measurements to be aggregated at different levels of granularity without redefining the delineations themselves. For example, with delineations named `Cortex:L1:proximal`, `Cortex:L1:distal`, and `Cortex:L2/3` three grouping levels are possible:
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-**Level 1** groups everything under `Cortex` into a single entry
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-**Level 2** groups by layer (`Cortex::L1` combines proximal and distal; `Cortex::L2/3` remains separate)
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-**Level 2** groups by layer (`Cortex:L1` combines proximal and distal; `Cortex:L2/3` remains separate)
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-**Level 3 (full)** reports each delineation individually
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The level-split prompt only appears when at least one delineation name contains the `::` separator. The _Non-delineated_ and _Unaffected paths_ categories always pass through unchanged regardless of the chosen level.
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The level-split prompt only appears when at least one delineation name contains the `:` separator. The _Non-delineated_ and _Unaffected paths_ categories always pass through unchanged regardless of the chosen level.
Copy file name to clipboardExpand all lines: _pages/plugins/snt/modeling.md
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{% include notice content=version %}
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Modeling in SNT is performed through [Cortex3D (Cx3D)](https://github.com/morphonets/cx3d) and [sciview](/plugins/sciview). Cx3D was developed in 2009 as a computational modeling tool for simulating neurodevelopmental processes and is well known for generative models of cortical circuits. The [Morphonets](http://morphonets.org) distribution of Cx3D was modified by {% include person id='kephale' %} to be compatible with SNT and the ImageJ ecosystem. This includes using [sciview](/plugins/sciview)for 3D visualization, and support for image-based modeling.
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Modeling in SNT is performed through [Cortex3D (Cx3D)](https://github.com/morphonets/cx3d) and [sciview](/plugins/sciview). Cx3D was developed in 2009 as a computational modeling tool for simulating neurodevelopmental processes, including cell division, migration, neurite outgrowth, and chemotaxis in 3D physical space. It is well known for generative models of cortical circuits.
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Currently, an [IDE](/develop/ides) is the most effective way to implement custom models, using the [minimal-cx3d-example-project](https://github.com/morphonets/minimal-cx3d-example-project) as a template. For more information refer to the [GitHub project page](https://github.com/morphonets/cx3d).
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Unlike electrophysiology simulators (e.g., [NEURON](https://www.neuronsimulator.org/)), Cx3D operates at the developmental time scale: it models how neurons grow and wire up, not how they fire. The [Morphonets](http://morphonets.org) distribution of Cx3D was modified by {% include person id='kephale' %} to be compatible with SNT. This includes using [sciview](/plugins/sciview) for 3D visualization, and support for image-based modeling.
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{% include img align="center" name="cx3d-sciview" src="/media/plugins/snt/cx3d-sciview.png" caption="Synthetic neuron generated using the *[Random Branching](https://github.com/morphonets/cx3d/blob/-/src/main/java/sc/iview/cx3d/commands/RandomBranchingDemo.java)* demo, accessible from sciview's *Demo* menu." %}
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## Key Cpabilities
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-**Morphogenesis**: Cells divide, migrate, and grow neurites in a 3D physical space governed by mechanical forces and chemical gradients
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-**Agent-based**: Each cell follows local rules; emergent network structure arises from those rules
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-**Developmental time scales**: Hours/days of neurodevelopment
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-**Encoded environmental cues**: Cues like chemical gradients/forces can be encoded by imagery
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> NB: Membrane biophysics and related cable equations are not considered in Cx3D simulations
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## Custom Models
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Currently, an [IDE](/develop/ides) is the most effective way to implement custom models, using the [minimal-cx3d-example-project](https://github.com/morphonets/minimal-cx3d-example-project) as a template. For more information refer to the [GitHub project page](https://github.com/morphonets/cx3d).
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