## Data Loader

Open or create a database, then import SWC files to begin analyzing dendritic structures

## Get Started

Open an existing database or create a new one to begin working with your neurons

### Open Existing Database

Load neurons from a previously saved SQLite database with full metadata

### Create New Database

Create a new empty SQLite database, then import SWC files from directories

## Database

0 neurons

### Computing Persistent Quadrics...

Warming up the math engine...

0 / 0 structures

### Persistent Quadrics Missing

Some structures are missing persistent quadric data. Compute now?

| No database

#### Directory Files

0 files

No directory loaded

#### Database Neurons

0 neurons
|

No database loaded

#### Merge Conflicts

0 conflicts found. 0 neurons will be imported automatically.

Apply to all:
Include subdirectories If neuron already exists

### SWC Files

#### Quick Actions

## Hexplot Viewer

Visualize eigenvalue distributions in hexagonal space

Directory:

### Compartment Mode

Whole Neuron Per Compartment Merged
Select compartments: Full Neuron Apical Dendrite Basal Dendrite Axon

Plot eigenvalue distributions as points in hexagonal space. For eigenvalue curve trajectories, use the Persistent Quadric Viewer.

### Plot Configuration

Title Metric
Show Box Plot Intersection Color By (optional)

#### Data Filters (select multiple)

Species
Load database to see options
Brain Region
Load database to see options
Cell Type
Load database to see options
Marker Size Marker Opacity 0.6
Width (px) Height (px)

### Visualization

Click "Generate Plot" to visualize eigenvalue distribution

Generating plot...

## Persistent Quadric Viewer

Visualize eigenvalue curve trajectories from database

Directory:

### Database

Path Criterion (for recompute)
Length Straightness Centrality Radius

### Select Neurons (0 selected)

Load a database to see neurons

### Compartment Mode

Whole Neuron Per Compartment Merged
Select compartments: Full Neuron Axon Basal Dendrite Apical Dendrite

### Plot Type

Eigencurves: Plot λ1, λ2, λ3 separately vs path distance
Hexplot: Plot trajectory in hexagonal eigenvalue space

### View Mode

### Path Depth (all)

0 = maximal path only, higher = include deeper branches

### Paths

### Display Options

λ1 (largest) λ2 (middle) λ3 (smallest)

Color by compartment

Shows all compartments with distinct colors

### Visualization

Select neurons from the list and click "Generate Plot" to visualize eigenvalue curves

Loading persistent quadric data...

## 3D Dendritic Viewer

Interactive 3D visualization of dendritic structures

File:

### Select File

Directory:
Select SWC File:
Server Directory Path:
Select SWC File:

0 SWC files found

or upload from your computer
Upload SWC File:
Vertices: 0 Edges: 0

### Compartment Selection

Select a compartment to view only that part, or "Full Structure" for the complete neuron

### Visualization

Point Size 0.5 Show Connections Highlight Branch Points Highlight Self-Intersections Scale by SWC Radius
3D Viewer Controls:
Left Click + Drag: Rotate view
Right Click + Drag: Pan (move) view
Middle Click + Drag: Pan (alternative)
Mouse Wheel: Zoom in/out
View Intersection:

### Subtree Analysis

Click on any vertex in the 3D view to select it and analyse the subtree rooted at that vertex.

Selected Vertex
ID: -
Position: -
Type: -
Subtree Statistics
Vertices: -
Edges: -
Leaves: -
Branch Pts: -
Length: -
Avg Edge: -
Max Path: -
Depth: -
Quadric Eigenvalues
Node: -
Edge: -
Highlight subtree in 3D view

Analysing subtree...

### 3D Visualization

Select an SWC file and click "Load 3D Structure"

Loading structure...

Vertex Information

## Data Explorer

Analyse dendritic structure properties

File:

### Select File

Directory:
Select SWC File:
Server Directory Path:

Enter a directory path on the server

Select SWC File:

0 SWC files found

or upload from your computer
Upload SWC File:

Select an SWC file from your computer

Upload Multiple Files (Directory):

Select a folder containing SWC files

Select from uploaded files:

0 SWC files uploaded

### Compartment Mode

Whole Neuron Per Compartment Merged
Select compartments:
Full Structure

### Display Options

Show Eigenvalue Analysis

### Neuroscience Analysis Tools

L S C R

#### Compare with another file:

Select an SWC file to analyse

#### Structure Overview

Total Vertices: -
Total Edges: -
Self-Intersects: -

#### Vertex Types

Root: -
Branch Points: -
Leaves: -
Regular: -

#### Spatial Extent

X Range: -
Y Range: -
Z Range: -
Total Span: -

#### Edge Quadric (Normalized)

lambda 1 (Max): -
lambda 2: -
lambda 3 (Min): -
Anisotropy: -
Planarity: -
Linearity: -

### Compartment: -

#### Compartment Overview

Vertices: -
Edges: -
Branch Points: -
Leaves: -
Total Length: -

#### Edge Quadric

l1 (Max): -
l2: -
l3 (Min): -
Anisotropy: -
Planarity: -
Linearity: -

### Vertices

Filter:

Index | Type | X | Y | Z | Has Parent
--- | --- | --- | --- | --- | ---

### Edge Analysis

#### Edge Lengths

Min: -
Max: -
Mean: -
Total: -

###
Sholl Analysis

#### Sholl Statistics

Max Intersections: -
Critical Radius: -
Enclosing Radius: -
Regression Coeff: -
Area Under Curve: -

###
L-Measure Metrics

#### Branching

N Stems: -
N Bifurcations: -
N Terminals: -
Max Branch Order: -
Avg Branch Order: -

#### Distances

Total Length: -
Max Euclidean: -
Max Path Distance: -
Avg Contraction: -

#### Angles

Avg Bifurcation Angle: -
Avg Local Bif Angle: -
Avg Remote Bif Angle: -
Partition Asymmetry: -
Hausdorff Dimension: -

###
Tortuosity Analysis

#### Summary

Average Tortuosity: -
Number of Branches: -

Start ID | End ID | Path Length | Euclidean | Tortuosity
--- | --- | --- | --- | ---

###
Morphology Features (ML Feature Vector)

#### Structure

Vertices: -
Edges: -
Branch Points: -
Terminals: -
Stems: -

#### Lengths

Total Length: -
Avg Branch Length: -
Max Branch Length: -
Max Euclidean: -
Max Path Distance: -

#### Branching & Angles

Max Branch Order: -
Avg Branch Order: -
Avg Bif Angle: -
Avg Tortuosity: -

#### Sholl Analysis

Sholl Max Intersections: -
Sholl Critical Radius: -
Sholl Enclosing Radius: -

###
Validation Report

#### Summary

Errors: -
Warnings: -
Vertices: -
Edges: -

#### Structure Issues

Roots: -
Disconnected Components: -
Duplicate Points: -
Zero-Length Edges: -

#### Issues

Severity | Category | Message | Vertices
--- | --- | --- | ---

###
Dendrogram

#### Dendrogram Stats

Max Depth: -
Max Path Distance: -
Width: -
Nodes: -

###
Path Decomposition

Paths
-
Criterion
-
Maximal Path Length
-
Total Length
-

Index | Type | Vertices | Edges | Length | Parent | Eigenvalues | Anisotropy
--- | --- | --- | --- | --- | --- | --- | ---

###
Neuron Comparison

#### Neuron 1

Vertices: -
Total Length: -
Branch Points: -
Terminals: -
Max Path Distance: -
Avg Tortuosity: -

#### Neuron 2

Vertices: -
Total Length: -
Branch Points: -
Terminals: -
Max Path Distance: -
Avg Tortuosity: -

### Selected Vertex

ID: -
Type: -
Position: -

### Subtree Statistics

-
Vertices
-
Edges
-
Terminal Points
-
Branch Points

### Geometry

Total Length: -
Avg Edge Length: -
Max Path Distance: -
Depth: -

### Quadric Eigenvalues

Edge Quadric
-

### Visualization

Highlight subtree in 3D view

Analysing subtree...

#### Subtree Structure

The subtree is highlighted in the 3D viewer. Use the checkbox in the left panel to toggle the highlight.

#### Vertices in Subtree

ID | X | Y | Z | Type
--- | --- | --- | --- | ---

#### Morphological Properties

Branching Ratio
-
Avg Branch Length
-
Strahler Number
-
Partition Asymmetry
-

## Settings

Configure metadata fields and application preferences

### Metadata Fields

Configure which metadata fields are available for neurons in this database. Built-in fields can be enabled/disabled but not deleted.

Loading fields...

### Application Logs

Configure logging level and manage application logs.

Log Level

Debug and Trace levels produce more detailed output

Log Retention
days

Session logs older than this are deleted on startup

### Visualization

Quadric Mode

Complement: perpendicular to edge, eigenvalues (L, L, 0). Direction: along edge, eigenvalues (L, 0, 0)

Plot background

Use transparent for exporting plots with no background

### Edit Field

Field Name (internal)

Used internally, no spaces allowed

Display Name

Shown to users in forms

Field Type
Options (one per line)

Enter each option on a new line

Description / Help Text
Default Value
Display Order

Lower numbers appear first

Enabled Required

### Log Viewer

### Metadata Field Configuration

Metadata fields allow you to store additional information about each neuron, such as species, brain region, cell type, and experimental conditions.

- Built-in fields (species, brain_region, etc.) can be enabled or disabled but not deleted.
- Custom fields can be created, modified, and deleted as needed.
- Select type fields provide a dropdown with predefined options.
- Required fields must be filled when creating or editing neurons.

Click on a field in the list to edit it, or use the "Add Custom Field" button to create a new one.

### No File Selected

Select a file from the Data Loader, 3D Viewer, or Data Explorer, then switch here to see detailed analysis.

## filename.swc

#### Structure Overview

Total Vertices: -
Total Edges: -
Root Nodes: -
Branch Points: -
Leaf Nodes: -
Self-Intersects: -

#### Spatial Extent

X Range: -
Y Range: -
Z Range: -
Bounding Diagonal: -

#### Edge Statistics

Min Length: -
Max Length: -
Mean Length: -
Total Length: -

#### Edge Quadric (Normalized)

lambda 1 (Max): -
lambda 2: -
lambda 3 (Min): -
Anisotropy: -
Planarity: -
Linearity: -

#### Compartments

Load a file to see compartments

### Neuroscience Analysis Tools

Click a tool to toggle its analysis panel

#### Sholl Analysis

Radius Step (um):
Computing Sholl analysis...
Total Intersections: -
Max Intersections: -
Max Intersection Radius: -
Ramification Index: -

#### L-Measure Compatible Metrics

Computing L-Measure metrics...
Branches: -
Bifurcations: -
Tips: -
Total Length: -
Avg Branch Length: -
Max Branch Length: -
Max Branch Order: -
Avg Branch Order: -
Asymmetry Ratio: -
Surface Area: -
Volume: -
Partition Asymmetry: -
Max Path Length: -
Avg Path Length: -
Max Euclidean Dist: -
Width: -
Height: -
Depth: -

#### Branch Tortuosity Analysis

Computing tortuosity indices...
Average Tortuosity: -
Min Tortuosity: -
Max Tortuosity: -
Std Dev: -

#### ML Feature Extraction

Extracting morphological features...

##### Basic Metrics

Vertices: -
Edges: -
Branch Points: -
Tips: -

##### Spatial Metrics

Width: -
Height: -
Depth: -

##### Topological

Max Branch Order: -
Avg Tortuosity: -

##### Quadric Metrics

Node Anisotropy: -
Edge Anisotropy: -

#### Morphology Validation

Strict Mode
Validating morphology...
Valid
Total Issues: -
Errors: -
Warnings: -
Info: -

#### Dendrogram View

Generating dendrogram...
Nodes: -
Edges: -
Total Height: -

#### Path Decomposition

Length Straight. Central. Radius
Computing path decomposition...
Paths: -
Criterion: -
Maximal Path: -
Total Length: -

Idx | Type | Verts | Length | Eigenvalues | Aniso.
--- | --- | --- | --- | --- | ---

## Population Comparison

Select and compare groups of neurons based on metadata criteria

### Define Populations

Create populations by filtering neurons based on metadata fields.

### Analysis Options

Distance Metric
Feature Set
Compartment Mode
Whole Neuron Per Compartment Merged
Select compartments: Soma Axon Basal Dendrite Apical Dendrite
MDS Dimensions
HCA Linkage Method

### Population Comparison Summary

Define populations and run analysis to see results.

### Top Discriminating Features

Features with largest effect sizes will appear here.

### Multidimensional Scaling (MDS)

Run analysis to generate MDS plot.

### Hierarchical Clustering Dendrogram

Run analysis to generate dendrogram.

### Dissimilarity Matrix

Run analysis to generate heatmap.

### Select SWC File

Choose a single SWC file to analyse

## filename.swc

#### Structure Overview

Total Vertices: -
Total Edges: -
Root Nodes: -
Branch Points: -
Leaf Nodes: -
Self-Intersects: -

#### Spatial Extent

X Range: -
Y Range: -
Z Range: -
Bounding Diagonal: -

#### Edge Statistics

Min Length: -
Max Length: -
Mean Length: -
Total Length: -

#### Edge Quadric (Normalized)

lambda 1 (Max): -
lambda 2: -
lambda 3 (Min): -
Anisotropy: -
Planarity: -
Linearity: -

#### Compartments

Load a file to see compartments

### Neuroscience Analysis Tools

Click a tool to toggle its analysis panel

#### Sholl Analysis

Radius Step (um):
Computing Sholl analysis...
Total Intersections: -
Max Intersections: -
Max Intersection Radius: -
Ramification Index: -

#### L-Measure Compatible Metrics

Computing L-Measure metrics...
Branches: -
Bifurcations: -
Tips: -
Total Length: -
Avg Branch Length: -
Max Branch Length: -
Max Branch Order: -
Avg Branch Order: -
Asymmetry Ratio: -
Surface Area: -
Volume: -
Partition Asymmetry: -
Max Path Length: -
Avg Path Length: -
Max Euclidean Dist: -
Width: -
Height: -
Depth: -

#### Branch Tortuosity Analysis

Computing tortuosity indices...
Average Tortuosity: -
Min Tortuosity: -
Max Tortuosity: -
Std Dev: -

#### ML Feature Extraction

Extracting morphological features...

##### Basic Metrics

Vertices: -
Edges: -
Branch Points: -
Tips: -

##### Spatial Metrics

Width: -
Height: -
Depth: -

##### Topological

Max Branch Order: -
Avg Tortuosity: -

##### Quadric Metrics

Node Anisotropy: -
Edge Anisotropy: -

#### Morphology Validation

Strict Mode
Validating morphology...
Valid
Total Issues: -
Errors: -
Warnings: -
Info: -

#### Dendrogram View

Generating dendrogram...
Nodes: -
Edges: -
Total Height: -

#### Path Decomposition

Length Straight. Central. Radius
Computing path decomposition...
Paths: -
Criterion: -
Maximal Path: -
Total Length: -

Idx | Type | Verts | Length | Eigenvalues | Aniso.
--- | --- | --- | --- | --- | ---

### 3D Preview

### CSV File Input

Rows: 0

### Plot Configuration

Title Metric
Color By (optional)
Width (px) Height (px)

### Visualization

Select a CSV file and click "Generate Plot" to visualize eigenvalue distribution

Generating plot...

Neuroscience Helper

### Intersecting Edges

Loading intersection data...

### Import Preview - Metadata

Apply to all:

### Importing Files

Importing... 0/0