IncucyteAI — Auto-Download Agent

Automatically download TIF images from the Incucyte live-cell imaging system via its SOAP API. Replaces the manual click-to-download workflow with a script that polls for new scans and saves them to a folder.

Requirements

• Python 3.10+
• Must be on the Imperial College London network (the Incucyte device is not internet-accessible)

Install

pip install zeep requests pillow numpy

Quick Start (GUI)

python incucyte_gui.py

1. Enter the Incucyte host IP and your credentials, click Login
2. Select one or more vessels from the list
3. (Optional) Click Select Wells to choose specific wells
4. Choose channel filters (Phase, Color 1, Color 2)
5. Set the output folder
6. Set Start from: "First scan" to get all historical images, "Today" for new ones only, or a custom date
7. Click Download Now for a one-shot download, or Start Watching to poll automatically

Quick Start (CLI)

# Test connectivity
python incucyte_downloader.py probe --host 129.31.116.189

# Login (saves credentials)
python incucyte_downloader.py login --host 129.31.116.189

# List experiments and vessels
python incucyte_downloader.py experiments

# Download all images from a vessel, starting from its very first scan
python incucyte_downloader.py download -v 38 -o ./images --start-from first

# Download from a specific date
python incucyte_downloader.py download -v 38 -o ./images --start-from 2026-03-01

# Watch mode: poll every 10 minutes for new scans
python incucyte_downloader.py watch -v 38 -o ./images -i 10 --start-from first

Features

• Parallel downloads — configurable number of worker threads (default 4)
• Green LUT for Phase — Phase contrast images are saved as green-channel RGB TIFs (toggle off with --no-green-lut)
• Start from any date — download from the vessel's first scan, today, or any custom date
• Progress dialog (GUI) — file count, progress bar, speed estimate, ETA, cancel button
• Window title updates — shows download progress and next-poll countdown when minimized
• Retry with backoff — transient network failures retry up to 3 times
• State tracking — already-downloaded images are skipped on subsequent runs
• Well & channel filters — download only specific wells and/or image channels
• Elapsed-time filenames — files named with elapsed time from experiment start (e.g., VID38_A1_1_024h30m.tif)
• Graceful shutdown — closing the window during watch mode stops cleanly

CLI Options

download

Flag	Description
-v, --vessel	Vessel ID to download
-o, --output	Output directory
-s, --start-from	first (all history), YYYY-MM-DD, or omit for today
-d, --date	Single date to download (YYYY-MM-DD)
-w, --wells	Well filter (e.g., A1, A1,B3, A1-D4)
-c, --channels	Channel filter (phase, color1, color2, all)
--workers	Parallel download threads (default: 4)
--no-green-lut	Disable green LUT for Phase images

watch

Same as download, plus:

Flag	Description
-i, --interval	Poll interval in minutes (default: 10)

File Structure

IncucyteAI/
  incucyte_downloader.py   CLI tool and core download logic
  incucyte_gui.py          Tkinter GUI
  CLAUDE.md                Agent context (for Claude Code)
  SETUP_PLAN.md            On-site deployment guide
  README.md                This file
  .gitignore               Excludes state files and WSDL
  .tmp/                    Config, state, captures (gitignored)

Setup at Imperial

See SETUP_PLAN.md for step-by-step instructions.