toolsandogh

A Python toolbox for iSCAT microscopy data analysis, developed by the Sandoghdar Division of the Max Planck Institute for the Science of Light (MPL).

Overview

toolsandogh provides a small, reusable library for loading, processing, analyzing, and storing microscopy videos. It is designed around a canonical 5D data model---T (time), C (channel), Z (slice), Y (row), X (column)---implemented as lazy xarray arrays backed by Dask.

Features

  • Lazy, out-of-core computation: Videos are kept as Dask arrays so you can work with datasets larger than memory.
  • Labeled, metadata-rich arrays: Results are xarray.DataArray objects with TCZYX dimensions and OME metadata.
  • Multiple microscopy formats: Read and write RAW/BIN, TIFF, OME-TIFF, OME-Zarr, ND2, and other formats supported by bioio.
  • Reusable analysis primitives: Rolling statistics, radial variance transform, synthetic data generation, and more.

Installation

This project uses the uv package manager. Clone the repository and run:

uv sync

To install in editable mode for development:

uv pip install -e ".[dev]"

Quick start

import toolsandogh as sand

# Load a video (any bioio-supported format or raw BIN/RAW file).
video = sand.load_video("movie.nd2")

# Apply a rolling average along the time axis.
smoothed = sand.rolling_average(video, window_size=5, dim="T")

# Save the result back to disk.
sand.store_video(smoothed, "smoothed.ome.tiff")

Use help(sand.load_video) or help(sand.store_video) for details on the available arguments.

Repository layout

  • src/toolsandogh/ --- the main Python package.
  • src/toolsandogh/tests/ --- pytest test suite.
  • DESIGN.md --- design conventions and coding standards.

Contributing

Please see DESIGN.md for coding conventions, documentation standards, and architecture decisions. In brief:

  • All public functions must be type-hinted and documented in numpydoc style.
  • Code is linted with ruff and type-checked with pyright.
  • Prefer free functions; keep data in xarray.DataArray/Dataset form.
  • Tests go in src/toolsandogh/tests/.

License

GPL-3.0-or-later.

Project links

Data verified by PyPI on Jul 20, 2026
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Key dates

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  • Released:
Newer release available (0.5.4)

2 maintainers

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Avatar for marcoheisig from gravatar.com marcoheisig Avatar for sandoghdarlab from gravatar.com sandoghdarlab

Credits

Author: Marco Heisig

GitHub Statistics

Data verified by PyPI on Jul 20, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License expression

GPL-3.0-or-later
View SPDX License List

Requires

Python >=3.12

Tags

tools utilities python microscopy

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