DART-MLCI: Aligning Blueprint and Physical Microfluidic Chip for Design-Aware and Real-Time Capable Live-Cell Image Analysis

Real-time microfluidic RoI image processing. DART-MLCI takes a raw microscopy frame, detects alignment markers, rotates and crops the RoI, masks the region of interest, and segments cells — automatically, for any chip design described by a single JSON config (fine alignment).

Time-constant microfluidic chip mapping. DART-MLCI allows to record several RoI positions on the microfluidic chip when its on the microscopy stage and aligns the microfluidic blueprint providing all RoI positions for any chip design described by a single JSON config (coarse alignment).

The repository covers two complementary capabilities:

• Fine algiment (Masking pipeline) — marker detection, pair matching, rotation correction, polygon masking, and ROI cropping.
• Coarse alignment (Map calibration) — affine alignment of the chip blueprint with microscope stage coordinates, so every chamber can be revisited automatically.

Installation

# From PyPI
pip install dart-mlci

# Or from source
git clone https://github.com/SMLCI/DART-MLCI.git
cd DART-MLCI
pip install ".[dev]"        # core + dev extras

YOLO marker-detection weights and the bundled sample images (~40 MB) are not shipped in the wheel. They download automatically on first use to ~/.cache/dart-mlci/ (Linux/macOS) or %LOCALAPPDATA%\dart-mlci\ (Windows). You can override the location with DART_ARTIFACTS_DIR=.... No manual download step is required.

Optional extras: pip install "dart-mlci[api]" for the FastAPI service, pip install "dart-mlci[segmentation]" to pull in Cellpose-SAM / Omnipose.

Quickstart: Python API

Run the marker detector on a bundled sample image:

# snippet: marker-detection
import cv2
from dart_mlci import ChipStructureLibrary, MarkerDetectionModel, sample_path

lib = ChipStructureLibrary.from_file(sample_path("chips/sak.json"), pixel_size=0.065789)
model = MarkerDetectionModel()

image = cv2.imread(str(sample_path("images/sak/0007.png")))
markers = model.predict_markers(image)
print(f"Detected {len(markers)} markers")  # e.g. "Detected 4 markers"

Compose the full pipeline as steps. lib(roi_id) returns the chamber's polygon and the expected pixel-space positions of its cross/circle markers (mgp):

# snippet: full-pipeline
import cv2
from dart_mlci import (
    ChipStructureLibrary,
    ImageRotationStep,
    MarkerDetectionStep,
    MarkerMatchingStep,
    RoIMaskingStep,
    sample_path,
)

lib = ChipStructureLibrary.from_file(sample_path("chips/sak.json"), pixel_size=0.065789)
_, polygon, mgp = lib("0000")  # any NormaleBox-inner ROI matches 0007.png

image  = cv2.imread(str(sample_path("images/sak/0007.png")))
detect = MarkerDetectionStep()
match  = MarkerMatchingStep(marker_group_pixel=mgp)
rotate = ImageRotationStep()
mask   = RoIMaskingStep(marker_group_pixels=mgp, roi_polygon=polygon)

data = mask(rotate(match(detect(image))))
cropped, chamber_mask = data["image"], data["mask"]

Process Your Own TIFF Stack

scripts/process_folder.py is the CLI for batch-processing time-lapse TIFF stacks. It works for a single stack just as well as a full experiment — point its folders dict at one subfolder.

1. Lay out your data

my_data/
├── my_chamber/
│   ├── stack_001.tif         # T x H x W, uint16
│   └── stack_002.tif

2. Write a minimal folder_config.json

{
  "input_dir": "my_data",
  "output_dir": "my_output",
  "pixel_size": 0.0928,
  "segmenter": "cellpose-sam",
  "folders": {
    "my_chamber": "NormaleBox-inner"
  }
}

Omit chip_config / model_path to use the auto-downloaded defaults (the SAK chip JSON and the bundled YOLO weights). Override either field with an absolute path if you have a custom chip.

Set pixel_size to your microscope's µm/px. To list the chamber types available in your chip JSON:

# snippet: list-chamber-types
from dart_mlci import ChipStructureLibrary, sample_path

lib = ChipStructureLibrary.from_file(sample_path("chips/sak.json"), pixel_size=0.065789)
print(list(lib.polygon_library))

3. Run

python scripts/process_folder.py \
    --config folder_config.json \
    --save-cropped \
    --render-stacks \
    --verbose

Useful flags:

4. What you get

Each stack produces stack.tif (instance labels), cells.csv (per-cell measurements), meta.csv (per-frame metadata), and — with --render-stacks — two MP4s. The full output schema is in docs/configuration.md.

Using a chip other than SAK? Author a new chip JSON — see Adapting to a new chip design.

Reproduce the Paper Experiment

A single command runs the full pipeline against the public DART dataset:

bash reproduce.sh            # smoke test (1 stack per folder, ~250 MB)
bash reproduce.sh --full     # full experiment (all stacks, ~9 GB)

The script creates a conda env, downloads the dataset and calibration data from Sciebo, calibrates the map, processes all seven chamber types, and validates the outputs. Per-step details are in docs/configuration.md.

Map Calibration

The second core contribution: aligning the chip blueprint with microscope stage coordinates so every chamber can be revisited automatically.

# Compute affine transform from 3 calibration images
python scripts/calibrate_map.py \
    --config calibration_config.json \
    --output calibrated_map.csv \
    --output-dir calibration_output/ \
    --verbose

# Validate against independent images
python scripts/validate_map.py \
    --config validation_config.json \
    --output-dir validation_output/ \
    --verbose

The calibration step in reproduce.sh invokes both. Validation reports per-point error in microns and pixels and produces a histogram + spatial error map.

REST API

pip install "dart-mlci[api]"
uvicorn dart_mlci.api.main:app --host 0.0.0.0 --port 8000
# Interactive docs at http://localhost:8000/docs

import base64, requests
b64 = base64.b64encode(open("image.tif", "rb").read()).decode()
resp = requests.post("http://localhost:8000/process-image",
                     json={"image": b64, "roi_id": "0050"})
print(resp.json()["chamber_type"])

Or via Docker: docker-compose up --build.

Visit http://localhost:8000/docs for interactive Swagger documentation of every endpoint. See docs/DOCKER_GUIDE.md for container deployment.

Adapting to a New Chip Design

The pipeline is chip-agnostic: it only needs one JSON describing chamber polygons, marker positions, and a blueprint map. Start from the bundled SAK config as a template (sample_path("chips/sak.json") resolves it on demand), then follow docs/CHIP_CONFIG.md for the full schema, polygon conventions, marker-detection trade-offs (reuse the bundled YOLO weights vs. retrain on new fiducials), and a validation checklist.

License

MIT — Copyright (c) 2026 Johannes Seiffarth, Forschungszentrum Jülich GmbH.

Citation

If you use DART-MLCI in your research, please cite:

@software{dart-mlci,
  author  = {Seiffarth, Johannes and Pesch, Matthias and Scholtes, Lukas and Kohlheyer, Dietrich and Scharr, Hanno and N{\"o}h, Katharina},
  title   = {DART: Aligning Blueprint and Physical Microfluidic Chip for Design-Aware and Real-Time Capable Live-Cell Image Analysis},
  year    = {2026},
  url     = {https://github.com/SMLCI/DART-MLCI}
}