Cortex.md
Local-first AI research vault

An AI research vault for Markdown you own.

Cortex.md captures web pages, Gmail, Drive, documents, and YouTube into an Obsidian-compatible vault on your disk. AI reads and links the material, then leaves a ledger of the model, credits, sources, snippets, and outputs.

Try the guided sample vault first, or install free with 25 monthly AI credits.

AI transparency ledger Research packs Context pack export Source refresh and diff Obsidian companion No ad tracking
Cortex.md side panel capturing "The Bitter Lesson" into a local Markdown vault
00Shipped now

Built past the clipper stage.

Cortex.md is now shaped around local file ownership, auditable AI, and context that can be reused by other tools. Capture is still fast; the differentiator is what the vault records after capture.

Activation

Guided first useful note

Use the sample vault or a real capture, run AI ingest, open the linked note, ask the first question, and inspect the graph.

Trust

AI transparency ledger

Every AI action records provider, model, credits, input files, snippets, source type, outputs, and a retention note.

Research

Evidence-grade packs

Save research runs as Markdown folders with claim/evidence tables, citation graphs, bibliographies, confidence, and stale-source warnings.

Agents

Context pack exporter

Create .cortex context packs with curated notes, a manifest, and prompt templates for Claude, ChatGPT, Cursor, and Codex.

Freshness

Source refresh and diff

Refresh captured sources, compare changed claims and citations, preserve raw history, and choose when to re-ingest.

Workspace

Obsidian companion

Read .cortex activity, hot cache, and provenance from inside Obsidian, then open Cortex actions against the current note.

01How it works

First useful note in minutes.

Onboarding now starts with a useful research loop: capture a source, run AI ingest, open the linked Markdown note, ask one grounded question, then inspect the graph and activity ledger.

01 · START

Sample vault or real source

Start from the guided demo vault before OAuth, or hit ⌘⇧S to capture a page, email, Drive doc, upload, or YouTube source.

02 · INGEST

Pick AI depth

Quick, standard, detailed, and max ingest levels make cost and output depth explicit. Each run writes frontmatter and an activity ledger row.

03 · OPEN

Read the linked note

AI tags, categorizes, extracts links, and writes Obsidian-compatible Markdown you can open in Cortex, Obsidian, VS Code, or git.

04 · ASK

Question and inspect

Ask a grounded question, review the citations, then inspect the graph and Activity trust center to see what AI used and created.

02The vault

Real markdown. Real files. Real disk.

Cortex.md writes to a folder you pick. Open it in Obsidian. Grep it. Commit it to a private git repo. Move it to a different machine. The vault is not a database we hold for you - it is just files.

  • Obsidian-compatible — frontmatter, wikilinks, tags. Drop-in vault.
  • Two-way sync — edit in Cortex.md or in your editor. Changes reconcile on focus.
  • Agent-readable — AGENTS.md, meta/hot.md, meta/index.md, and .cortex JSONL files document the vault contract.
  • Full-text search — MiniSearch across every captured note, plus curated context packs for external AI.
  • Portable forever — nothing proprietary. Uninstall and your notes are still there.
~/Documents/vault
342 notes · 1,847 links
inbox2 new
📄2026-04-30-neuralink-tim-urban.mdNEW
📄2026-04-30-rust-ownership.md2m ago
research
📄brain-computer-interfaces.md
📄whole-brain-emulation.md
📄embodied-cognition.md
engineering
📄borrow-checker-notes.md
📄distributed-systems-101.md
recipes14
daily62
📄README.md
03On-board intelligence

Ask, research, and package evidence from the same vault.

Two AI surfaces, both included in your plan. Ask answers questions from notes you've already captured, with wikilink citations. Research writes sourced notes and can save the run as a portable research pack with claim/evidence tables, citation graphs, source confidence, and stale-source warnings.

⌘ ASK

Question your vault

Type any question. Cortex.md retrieves the most relevant notes (semantic + lexical), feeds them to a hosted model, and answers with [[wikilink]] citations back to the source notes. The Activity ledger records which excerpts were used.

  • Grounded — answers cite exact note titles, not invented sources.
  • Hybrid retrieval — MiniSearch lexical + optional embeddings for semantic match.
  • Auditable — provider, model, credits, retrieved files, and output notes are recorded for every AI turn.
  • Honest about gaps — if your vault doesn't cover it, it tells you what's missing.
Ask your vault
claude-sonnet-4-6
What did I learn about brain-computer interfaces last spring?
Retrieved 4 notes · 1,847 tokens 2 credits
0.92 Brain-Computer Interfaces 0.87 Neuralink and the Brain's Magical Future 0.71 Whole-Brain Emulation 0.64 Embodied Cognition

Three threads ran through what you read on BCIs in spring 2026:

1. Bandwidth is the bottleneck. Current invasive electrodes max out around a few thousand neurons; [[Neuralink and the Brain's Magical Future]] argues a useful "whole-brain interface" needs ~10⁶ channels — a four-order-of-magnitude gap.

2. Read is easier than write. Decoding intent from motor cortex is largely solved; closed-loop stimulation that feels like a thought rather than a buzz remains open ([[Brain-Computer Interfaces]], §3).

3. Substrate independence is the long bet. [[Whole-Brain Emulation]] reframes BCIs as the gradual half of a Ship-of-Theseus migration off biological wetware.

📡 Auto-research Manual
40 / 1,000 credits this month
CRISPR base editing — clinical trials 2025
Searching the web via Perplexity 1.3s
Gathered 11 sources · 8 cited 2.1s
Extracted 6 entities, 4 concepts 0.4s
Writing research/crispr-base-editing-2025.md
Saving research pack and citation graph
title: CRISPR base editing — clinical trials 2025
category: Research/Biotech
researched_at: 2026-04-30T14:08
model: sonar-pro
ai_credits: 15
citations: 8
## Summary
Base editing reached pivotal trial readouts in [[Sickle Cell Disease]] and familial hypercholesterolemia. [1][3]
## Entities
· Verve Therapeutics · Beam Therapeutics · David Liu
## Citations
[1] nature.com/articles/d41586-025-…
[2] nejm.org/doi/full/10.1056/…
[3] statnews.com/2025/03/…
⚛ AUTO-RESEARCH

Type a topic, get a sourced artifact

Cortex.md's research agent dispatches to Perplexity Sonar, gathers and dedupes citations, extracts entities and concepts, then writes an Obsidian-compatible note with frontmatter and inline cites. Save the run as a research pack when you need evidence you can hand off.

  • Web-grounded — every claim ends in a numbered citation back to a real URL.
  • Evidence-grade — packs include claim/evidence tables, citation graphs, bibliographies, and source notes.
  • Graph-aware — new notes link to existing entities and concepts automatically.
  • Capped & pausable — a hard monthly credit ceiling stops the agent before it can run away.
  • Deep mode — recursively researches stub links it created, up to your call cap.
04Knowledge graph

See how everything you've read connects.

Every wikilink becomes an edge. The side panel renders a force-directed view of the whole vault — clusters surface naturally, orphans surface what needs linking.

05AI ledger & control

Activity is now the trust center.

Cortex.md only sees a source when you ask it to. The extension uses activeTab + scripting for pages, and every AI action is mirrored into note frontmatter and .cortex activity files.

Transparency ledger

  • Provider, model, credits, source type, inputs, snippets, outputs, and retention note are visible in Activity.
  • Generated notes mirror ledger fields in frontmatter so provenance travels with the Markdown file.
  • .cortex/activity.jsonl records the same audit trail for Obsidian plugins and external agents.
  • No ad tracking. Website measurement is limited to privacy-conscious page and CTA events; account usage metadata supports billing, quotas, reliability, and support.

Managed AI, no setup

Best-in-class models, included in your plan. Hit your monthly credit cap and Cortex pauses expensive actions - no surprise bills.

Anthropic Claude
Default model · best at reasoning
claude-sonnet-4-6
OpenAI GPT
Available on Pro
gpt-5.4
06Built for the keyboard

Capture without leaving the page.

S
Save page
The whole article, readability-cleaned, into inbox/.
E
Save selection
Just the highlighted passage, with a backlink to the source URL.
K
Search vault
Full-text search across every note, from the popup. Open results in the side panel.

Install the AI research vault for local Markdown.

Capture a source, audit the AI work, save research packs, export context packs, and keep the same files in Obsidian, VS Code, git, or any editor.

v0.1 · open beta · Chromium · Firefox port soon