About the Insight Journal

Sustainable Open Science with Web3 Technology

The Insight Journal 3 (IJ3) is an innovative undertaking to bring sustainability to reproducible research through the power of decentralized Web3 technologies.

The IJ3 is built on a foundation of proven technologies:

• Git: Version control and collaborative development
• InterPlanetary File System (IPFS): Decentralized storage
• Ethereum: Blockchain-based verification and provenance

It's Merkle trees all the way down.

These technologies all share a common foundation: Merkle trees, which provide cryptographic verification and tamper-proof records. Every change, every version, every contribution is permanently and verifiably recorded.
Post-publication manipulations are impossible without detection. This ensures integrity, transparency, and trustworthiness

FAIR by Design

The platform's architecture ensures all research objects are:

• Findable: Indexed in OpenAlex, CrossRef, and Google Scholar
• Accessible: Open access with no paywalls or publication charges
• Interoperable: Standards-compliant metadata and identifiers
• Reusable: Open licenses, complete documentation, and included dependencies

Interactive Visualizations with ITK-Wasm and NiiVue

Building on the Insight Toolkit (ITK), the journal supports browser-based visualization of medical imaging datasets through ITK-Wasm and NiiVue. This enables:

• Direct 3D visualization of medical images in web browsers
• Interactive exploration of imaging data without specialized software
• Cross-platform compatibility without installation requirements

DeSci Nodes Platform

The Insight Journal operates on DeSci Nodes, a decentralized science publication platform that enables researchers to publish and share research objects—not just manuscripts, but complete packages of data, code, visualizations, and documentation.

Key Features of DeSci Nodes

• Research Objects: Publish manuscripts alongside data, code, images, and other artifacts in a single, coherent package
• Version Control: Track the evolution of research from initial ideas through publication and beyond
• Persistent Identifiers (DPIDs): Content-addressed identifiers that never break or require maintenance
• Decentralized Storage: Content stored across multiple nodes on IPFS, ensuring availability and preservation
• CrossRef Integration: Minting DOIs for published works while maintaining deterministic resolution through DPIDs
• ORCID Integration: Automatic credit for authors and reviewers
• Attestations: Verifiable claims about research quality, openness, and reproducibility

Addressing Traditional Publishing Limitations

Traditional publishing suffers from:

• Link rot: Within 3 years, 50% of URIs in scientific publications break; nearly all break within a decade
• Content drift: URLs that resolve but point to different content
• DOI failures: Traditional DOIs fail to resolve correctly about 50% of the time
• Data silos: Centralized repositories create single points of failure

DeSci Nodes with DPIDs solves these problems through content-addressed storage, distributed architecture, and cryptographic verification.

Web3 Principles

The IJ3 applies Web3 technologies based on three core principles:

1. Verifiability

Every component of a research object receives a cryptographic hash-based decentralized persistent identifier (DPID) that serves as both identifier and integrity check. Any modification—even a single pixel or letter—produces a different hash, ensuring you always retrieve exactly the version you expect.

2. Decentralization

Content is stored across multiple independent nodes on the InterPlanetary File System (IPFS). This distributed model follows the principle that "many copies keep things safe." Unlike centralized repositories that create single points of failure, decentralized storage ensures content remains available even if individual nodes go offline.

3. Incentive Engineering

Blockchain-based provenance creates tamper-proof records of contributions. This enables reputation-based systems and potentially tokenized rewards for quality peer review, aligning individual incentives with the broader goal of scientific progress.

Modern Publishing with MyST for the AI Age

The Insight Journal leverages MyST (Markedly Structured Text) to enable rich, interactive content that transforms articles from static PDFs into engaging, explorable research artifacts.

MyST Markdown's structured yet human-readable format makes research exceptionally accessible to AI systems and large language models (LLMs). Unlike proprietary formats or PDFs that obscure content structure, MyST preserves semantic meaning through its markup—equations remain interpretable, code blocks are clearly delineated, and citations maintain their relationships. This machine-readability enables AI agents to accurately extract methodologies, reproduce analyses, generate summaries, and synthesize findings across multiple papers.

As research increasingly leverages AI for literature review, meta-analysis, and automated hypothesis generation, MyST's transparent structure ensures that published knowledge remains computationally accessible for decades to come, bridging human scholarship and artificial intelligence.

MyST Example

Here's an example of MyST frontmatter showing the rich metadata and easy markdown editing features available:

---
title: The Importance of Open Access in Scientific Publications
subtitle: A Template for MyST Markdown Articles in the Insight Journal
abstract: |
  This document describes a new algorithm implemented using the Insight Toolkit
  ITK (itk.org)..

  This paper is accompanied with the source code, input data, parameters and
  output data that the authors used for validating the algorithm described in
  this paper. This adheres to the fundamental principle that scientific
  publications must facilitate reproducibility of the reported results.

keywords:
  - open science
  - reproducible research

abbreviations:
  FAIR: Findable, Accessible, Interoperable, and Reusable
  ITK: Insight Toolkit
  WASM: WebAssembly
---

Automatic detection and tracking of the solar spot movements are of fundamental
importance for allowing the authors to dedicate more time to perfectioning
optical instruments and less time to the supervised acquisition of reliable
data.

```{warning}
The reader should be warned that direct observation of the sun without proper
equipment may result in personal injury, loss of vision and burned brains.
```

For questions on the basis of the scientific method the reader is referred to
{cite}`Popper2002,Popper1971`.

## Why Image Processing Papers must include Source Code, Images and Parameters

Papers to the Insight Journal are written in the spirit of facilitating and
encouraging readers to perform replication of work. In this sense, the Insight
Journal is compliant with essential concepts of the scientific method.

### Including Figures

```{figure} ./assets/RegistrationComponentsDiagram.png
:name: fig-registration-components
:width: 80%

The basic components of the registration framework are two input images, a transform, a metric, an interpolator and an optimizer.
```

### Mathematical Equations

To support shape-guidance, the generic level set equation
({eq}`eqn-shape-influence-term`) is extended to incorporate a shape guidance
term:

```{math}
:label: eqn-shape-influence-term
\xi \left(\psi^{*}(\mathbf{x}) - \psi(\mathbf{x})\right)
```

### Code Examples

```python
import itk

# Load an image
image = itk.imread('data/img1.png')
```

Author-Friendly Features

MyST provides a modern authoring experience with powerful features for scientific publishing:

• Rich Scientific Content: Native support for figures, equations, citations, cross-references, and bibliographies using familiar Markdown syntax
• Multiple Export Formats: Single source generates HTML, PDF (via Typst—no LaTeX required), Microsoft Word (DOCX), and MECA archives for journal submission
• Interactive Visualizations: Embed dynamic HTML elements, 3D visualizations, and executable code directly in manuscripts
• Reproducible Environments: Integrated dependency management with Pixi ensures consistent builds across systems
• Live Preview: Development server with hot reload lets you see changes instantly as you write
• Source Code Integration: Include and test C++, Python, or other code alongside your manuscript with automated validation
• Version Control Ready: Plain text Markdown format works seamlessly with Git for collaboration and tracking changes

Getting Started

Authors can begin with the Insight Journal Template, which provides a complete authoring environment including example code, data, and documentation. The template supports both pure documentation projects and those with executable C++ or Python code.