Self-hosted research workspace

Neuroimaging workflows.
One Docker install.

Inspect MRI data, organize cases, run FastSurfer, and explore results with a viewer-aware assistant.

Install NeuroCade Explore sample case GitHub

NeuroCade sample case workspace showing MRI views, layers, and assistant panel

One workspace

From source image to
surface reconstruction

Keep case organization, interactive review, processing, and results together in a browser-based research environment.

Cases

Research data workspace

Create workspaces and cases, then import NIfTI volumes, DICOM ZIP archives, or existing FreeSurfer outputs.

Data and outputs persist in a host directory you configure.

Viewer

Volumes, labels, and surfaces

Review MRI volumes and segmentation overlays alongside cortical surfaces, with synchronized navigation and label lookup.

Load FastSurfer outputs directly into the active case.

Processing

FastSurfer built in

Launch FastSurfer cortical reconstruction and segmentation from the interface and follow long-running job status.

Current configured analysis runtime: FastSurfer.

Integrated processing

FastSurfer,
ready in the workspace

Run structural MRI segmentation and surface reconstruction from the active case, then review generated volumes, labels, statistics, and surfaces in the same interface.

FastSurfer Structural image analysis

Whole-brain segmentation

Corpus callosum morphometry

Cerebellum subsegmentation

Hypothalamus subsegmentation

Lesion-robust processing

Cortical surface reconstruction

Viewer-aware assistant

Work with the
active case in context

The optional assistant can inspect case files, control the viewer, read segmentation statistics, and launch configured workflows.

Connected to the active case

Ask about the volume, segmentation, surface, or label currently under review.

Actions, not just answers

Run configured tools, query measured statistics, and load generated results back into the viewer.

Your choice of provider

Configure OpenAI-compatible, Anthropic, Google, or Ollama models—or install without an LLM.

Assistant

Report the left and right hippocampal volumes from the FastSurfer segmentation.

NeuroCade I read the measured segmentation statistics for the active case.

Left hippocampus3,182 mm³
Right hippocampus3,409 mm³

Focus the viewer on the left hippocampus.

NeuroCadeThe crosshair is now centered on the left hippocampus and its segmentation label is highlighted.

Ask about the active case…

How it runs

A reproducible stack,
without the setup maze

The web interface, API, and background jobs ship together. Processing tools run through a dedicated container runtime.

01 / Browser

NeuroCade UI

Open the workspace from a local machine or an internally deployed server.

02 / Docker

Single app container

The built web UI, API, job worker, and Apptainer runtime ship in one published image.

03 / Storage

Mounted host data

Cases, outputs, tool images, and the SQLite database persist outside the app container.

04 / Apptainer

Neuroimage Containers

Run neuroimaging packages, such as FastSurfer, against the active case data. A large catalogue of tools is provided by NeuroDesk.

Know your data boundary. Image processing and case storage run on the host you configure. If you enable an external AI provider, assistant requests are sent according to that provider’s configuration and policies. Choose Ollama for a host-local model, or install with --llm-provider no-llm.

Quick install

Containerized install,
one command away.

The installer creates the local configuration and data directories, pulls the published image, downloads the prepared sample case, and starts NeuroCade.

The default local profile binds to your machine and opens at http://localhost:8000. The installer manages a small host-side bridge (Python/uv) automatically — no manual Python, Node.js, or Docker Compose setup is required.

Deployment

Runtime

Assistant

Version

Run this command

bash <(curl -fsSL https://raw.githubusercontent.com/Deep-MI/NeuroCade/main/scripts/install.sh) --mode local --runtime apptainer --llm-provider no-llm

PrerequisiteRootless Apptainer (auto-preferred on Linux; falls back to Docker if unavailable)

Browser locationhttp://localhost:8000

AI setupDisabled (--llm-provider no-llm)

Read the installation guide ↗ · Versioned releases ↗

Neuroimaging workflows.One Docker install.

From source image tosurface reconstruction