Cortex.md
v0.1 · open beta · local-first

Capture the web. Own the file.

Cortex.md is a Chromium extension that turns every page you save into plain markdown on your disk — categorized, cross-linked, and graphed by managed AI included in your plan. No lock-in. Just a folder you can open in Obsidian.

Markdown on disk Obsidian-compatible AI included No telemetry
waitbutwhy.com/2017/04/neuralink.html

Neuralink and the Brain's Magical Future

Suppose, in the next 30 years, a tiny implantable mesh becomes available that lets you exchange information with computers as fast as you can think.

A whole-brain interface would let humans access the cloud as readily as we now access our own memories. We'd think a question, and the answer would arrive — not on a screen, but inside our heads.

~/vault/research/neuralink.md
saved · 0.3s
title: Neuralink and the Brain's Magical Future
source: waitbutwhy.com
captured: 2026-04-30T14:02
tags: [bci, futures, urban]

# Neuralink and the Brain's Magical Future

> A whole-brain interface would let humans access the cloud as readily as we now access our own memories.

Related: [[Brain-Computer Interfaces]] · [[Whole-Brain Emulation]]

#research/bci   #longread
01How it works

Four steps from web page to wikilinked note.

Capture is one keystroke. Everything downstream — readability, markdown conversion, AI categorization, link extraction — runs locally in the extension's service worker.

01 · CAPTURE

Page or selection

Hit ⌘⇧S on any page, or right-click any text. Mozilla Readability strips the chrome.

02 · CONVERT

To clean markdown

Turndown produces faithful markdown with frontmatter — title, source, capture time, tags. Lands in inbox/.

03 · ORGANIZE

AI files it for you

Captures get tagged, categorized, and moved out of the inbox — Auto or Manual. Powered by your monthly credits.

04 · LINK

Wikilinks & graph

Cross-references between notes form a force-directed graph. Click any node to jump in.

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's 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.
  • Full-text search — MiniSearch across every captured note.
  • 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
03Knowledge 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.

342 nodes · 1,847 edges
All Tags Orphans
Brain-Computer Interfaces
Neuralink
Whole-Brain Emulation
Rust Ownership
Borrow Checker
Distributed Systems
Sourdough
Tartine Method
04On-board intelligence

A research agent and a Q&A oracle, both pointed at your vault.

Two AI surfaces, both included in your plan. Ask answers questions from notes you've already captured, with wikilink citations. Auto-research types a topic, and Cortex.md writes a fully-linked note from the open web — entities, concepts, citations and all.

⌘ 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. Only the retrieved excerpts and your question leave your machine.

  • Grounded — answers cite exact note titles, not invented sources.
  • Hybrid retrieval — MiniSearch lexical + optional embeddings for semantic match.
  • 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 $0.0021
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
$0.21 / $20.00 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
Linking to existing notes
title: CRISPR base editing — clinical trials 2025
category: Research/Biotech
researched_at: 2026-04-30T14:08
model: sonar-pro
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 note

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 — and links it into your existing graph.

  • Web-grounded — every claim ends in a numbered citation back to a real URL.
  • 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.
05Privacy & control

Your disk. Your control. Your credit budget.

Cortex.md only sees a page when you ask it to. The extension uses activeTab + scripting instead of host permissions, so it can't read a page until you tell it to.

Privacy posture

  • Vault content stays on your disk. No syncing service.
  • Sign in once with email — no passwords, no API keys to manage.
  • Page content is sent to AI only when you trigger a capture — never in the background.
  • No telemetry. No analytics. The extension only makes outbound calls when you trigger an action.

Managed AI, no setup

Best-in-class models, included in your plan. Hit your monthly credit cap and we pause — no surprise bills.

Anthropic Claude
Default model · best at reasoning
claude-sonnet-4-6
OpenAI GPT
Available on Pro
gpt-4.1
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.

Stop bookmarking. Start a vault.

One folder, one keystroke, and a brain-shaped graph of everything you've read. Start free — upgrade when you need more credits.

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