🔬 PathoLens Digital Pathology Workstation

PathoLens is a digital pathology workstation & AI workspace with a command-line launcher supporting Local Machine and Google Colab Cloud VM execution backends.

🚀 Key Features

• Dual Deployment Target: Run completely locally on your hardware, or spin up a free Google Colab GPU-accelerated cloud VM with one command.
• Zero-friction Colab Deploy (Zero Code Uploads): The CLI uses PyPI directly. Instead of slow zip uploads of the codebase, it initiates a PyPI installation (uv pip install) over Google's datacenter backbone (under 5 seconds) and only uploads the locally compiled static Next.js frontend (~6MB static.zip).
• Dynamic Slide Directory Configuration: Switch slide folders dynamically inside the browser UI Settings modal without having to restart the backend. Point it to local directories (e.g. /home/prime/slides) or Google Drive paths (/content/drive/MyDrive/...).
• Edge AI Diagnostics: Supports local execution of the gemma-4-E2B-it-litert-lm LiteRT model for local digital pathology clinical questions and diagnostics.

📦 Installation

To install the CLI globally using uv:

uv tool install patholens

🛠️ Usage

Simply run:

patholens launch

This launches the onboarding wizard in your terminal:

 █▀█ █▀█ ▀█▀ █▄█ █▀█ █   █▀▀ █▄ █ █▀
 █▀▀ █▀█  █  █ █ █▄█ █▄▄ ██▄ █ ▀█ ▄█ cli v2.0.7
 🔬 Digital Pathology Workstation & AI Workspace

 }  Environment: Cloud-Scalable / Multi-Tenant Ready
 }  Local Fallback: SQLite + Local Slide Storage

? Where would you like to run the PathoLens backend?
  1) Local Machine (Your computer's CPU/GPU)
  2) Google Colab VM (Free cloud CPU/GPU accelerators)

Option 1: Local Machine

Runs a local FastAPI backend and serves the Next.js frontend statically.

• Local AI option: You can choose to download the litert_lm package and cache the gemma-4-E2B-it-litert-lm model for local inference.
• Launch link: The CLI automatically opens your default browser at http://localhost:8000.

Option 2: Google Colab VM

• Drive Integration: Prompts you to mount your Google Drive on the VM.
• Fast Setup: Installs patholens from PyPI, uploads and extracts the frontend static.zip, installs slide bindings (libopenslide0), and opens a Cloudflare secure tunnel.
• Direct Browser Launch: The CLI automatically grabs the public *.trycloudflare.com tunnel URL and opens it in your web browser.

⚙️ Slide Directory Configuration

You can configure the active slide folder inside the browser UI dashboard.

1. Click the Settings gear icon in the header.
2. Input the absolute path to your slide directory (e.g. /content/drive/MyDrive/Slides on Colab, or a local directory).
3. Click Save Settings. The backend updates its active path on the fly and immediately lists the .svs files found in the folder.