mrsnappy 0.4.0

Fluorescent puncta detection for 2D microscopy images and 3D z-stacks.

SNAPpy

SNAPpy detects fluorescent puncta in 3D microscopy z-stacks and native 2D microscopy images. It uses a two-stage workflow:

1. Stage 1 finds candidate puncta with LoG or h-max local-maximum detection.
2. Stage 2 fits each candidate, measures interpretable local features, and uses an SVM to remove false candidates.

SNAPpy does not ship with trained model files. First optimize a model from labeled images, then use that model.joblib file to detect puncta in new images.

Names

Name	Meaning
SNAPpy	Project and repository name
mrsnappy	PyPI package, Python import, and terminal command

The PyPI name snappy is already used by an unrelated project, so this package uses mrsnappy.

Install

Install the current GitHub version:

python -m pip install "git+https://github.com/marcorojas-cessa/SNAPpy.git"

Or install the latest PyPI release:

python -m pip install mrsnappy

Check the command:

mrsnappy --help

For development:

git clone https://github.com/marcorojas-cessa/SNAPpy.git
cd SNAPpy
python -m pip install -e ".[dev]"
pytest

SNAPpy is CPU-based and does not require a GPU.

Quick Start

Create an editable config:

mrsnappy init-config --output config.yaml

The default config is the benchmark-tested starting point used for the SNAPpy publication work: h-max candidate detection, physical-unit smoothing/background sweeps, a 300 nm candidate-to-label matching radius, and interpretable SVM feature packs. Before using it on other microscope data, confirm or replace the physical spacing values:

pipeline_defaults:
  image_dimensionality: 3
  xy_spacing_nm: 128.866  # replace if your xy pixel spacing differs
  z_spacing_nm: 300.0     # replace if your z-step spacing differs

For native 2D images, set image_dimensionality: 2, set xy_spacing_nm, and use fit_method: 2D Gaussian. In 2D mode z_spacing_nm is not required and z-only Stage 2 features are omitted rather than filled with fake values.

Optimize a model from labeled training and validation images:

mrsnappy optimize \
  --dataset-root /path/to/labeled_dataset \
  --out-dir /path/to/model \
  --config config.yaml

Detect puncta in one new image:

mrsnappy detect \
  --model /path/to/model/model.joblib \
  --input /path/to/image.tif \
  --output /path/to/detections.csv

Detect puncta in a folder:

mrsnappy detect \
  --model /path/to/model/model.joblib \
  --input /path/to/images \
  --output /path/to/detections

For folder input, SNAPpy writes one CSV per image using the image stem. For example, cell_A_003.tif becomes cell_A_003.csv.

Labeled Dataset Layout

mrsnappy optimize currently uses fixed-split optimization. The dataset root must contain train/ and val/ folders:

labeled_dataset/
  train/
    image_001.tif
    image_001.csv
    image_002.tif
    image_002.csv
  val/
    image_101.tif
    image_101.csv

Each image must be either a 3D TIFF or, with pipeline_defaults.image_dimensionality: 2, a native 2D TIFF. For 3D images, each same-stem CSV must contain x, y, and z columns in voxel coordinates. For 2D images, CSV labels may contain x,y, y,x, or axis-0,axis-1 style columns; internally SNAPpy stores 2D coordinates in image-axis order (y,x).

Detection CSVs are dimensionality-aware: 3D output uses x,y,z,score, while 2D output uses x,y,score.

SNAPpy uses train/ to fit the Stage 2 SVM. It uses val/ to choose Stage 1 settings, Stage 2 feature/SVM settings, and the final SVM decision threshold. Held-out test scoring should be done outside SNAPpy by running mrsnappy detect and comparing detections to test labels.

Optimize Outputs

Optimization writes:

model/
  model.joblib
  model_config.json
  model_summary.md
  optimization_splits.csv

• model.joblib: trained model used by mrsnappy detect.
• model_config.json: machine-readable record of the exact config, selected model, selected features, validation metrics, Stage 1 shortlist, and near-tie Stage 2 finalists.
• model_summary.md: human-readable summary of the optimized model.
• optimization_splits.csv: exact train/validation image and label paths used during optimization.

Official SNAPpy intentionally keeps outputs compact. Benchmark-specific files such as per-image test metrics, resource metrics, localization offsets, or candidate-level audit tables should be produced by benchmark wrapper code, not by the core SNAPpy optimizer.

Detect Output

Detection CSV files contain:

detection_id,x,y,z,score
1,42.3,88.1,12.0,1.74
2,51.9,91.5,13.2,0.62

Coordinates are voxel coordinates. z is the stack axis.

How SNAPpy Works

The short version:

1. Read the 3D TIFF stack.
2. Optionally subtract background.
3. Normalize the image, usually by robust z-score.
4. Optionally smooth the image for Stage 1 detection.
5. Find candidate puncta with LoG or h-max local maxima.
6. Fit local Gaussian-style models around candidates.
7. Measure intensity, sigma, fit-quality, contrast, morphology, and distortion features.
8. Use the optimized SVM and threshold to keep likely true puncta.
9. Write final detections.

See docs/workflow.md for the full method explanation and docs/cli_api.md for the complete command and config reference.

Documentation

• Installation
• CLI/API and config reference
• Workflow
• Model files
• Hardware guidance
• Release notes

Repository Scope

This repository contains the installable SNAPpy package, documentation, examples, and tests. Raw microscopy data, trained models, benchmark result trees, cluster logs, and manuscript files are intentionally excluded.

Citation

If you use SNAPpy in a publication, cite the associated manuscript once available.