Quadrix Desktop - Dendritic Analysis Platform

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

Directory Files

0 files

No directory loaded

Database Neurons

0 neurons

No database loaded

Hexplot Viewer

Visualize eigenvalue distributions in hexagonal space

Directory:

Compartment Mode

Whole Neuron Per Compartment Merged

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

Plot Configuration

Title Metric Color By (optional)

Data Filters (select multiple)

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:

Visualization

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

3D Dendritic Viewer

Interactive 3D visualization of dendritic structures

File:

Select File

Directory:

Select SWC File:

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

Subtree Analysis

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

3D Visualization

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

Loading structure...

Data Explorer

Analyse dendritic structure properties

File:

Select File

Directory:

Select SWC File:

Compartment Mode

Whole Neuron Per Compartment Merged

Display Options

Show Eigenvalue Analysis

Neuroscience Analysis Tools

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: -

Vertices

Filter:

Index	Type	X	Y	Z	Has Parent

Edge Analysis

Edge Lengths

Min: -

Max: -

Mean: -

Total: -

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: -

Path Decomposition

Paths

-

Criterion

-

Maximal Path Length

-

Total Length

-

Index	Type	Vertices	Edges	Length	Parent	Eigenvalues	Anisotropy

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

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

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

Path Decomposition

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

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.

Get Started

Open Existing Database

Create New Database

Database

Computing Persistent Quadrics...

Persistent Quadrics Missing

Directory Files

Database Neurons

Merge Conflicts

SWC Files

Quick Actions

Compartment Mode

Plot Configuration

Data Filters (select multiple)

Visualization

Database

Select Neurons (0 selected)

Compartment Mode

Plot Type

View Mode

Path Depth (all)

Paths

Display Options

Visualization

Select File

Compartment Selection

Visualization

Subtree Analysis

3D Visualization

Select File

Compartment Mode

Display Options

Neuroscience Analysis Tools

Compare with another file:

Structure Overview

Vertex Types

Spatial Extent

Edge Quadric (Normalized)

Compartment: -

Compartment Overview

Edge Quadric

Vertices

Edge Analysis

Edge Lengths

Sholl Analysis

Sholl Statistics

L-Measure Metrics

Branching

Distances

Angles

Tortuosity Analysis

Summary

Morphology Features (ML Feature Vector)

Structure

Lengths

Branching & Angles

Sholl Analysis

Validation Report

Summary

Structure Issues

Issues

Dendrogram

Dendrogram Stats

Path Decomposition

Neuron Comparison

Neuron 1

Neuron 2

Selected Vertex

Subtree Statistics

Geometry

Quadric Eigenvalues

Visualization

Subtree Structure

Vertices in Subtree

Morphological Properties

Metadata Fields

Application Logs

Visualization

Edit Field

Log Viewer