deepblink 0.0.4

Threshold independent detection and localization of diffraction-limited spots.

deepBlink

Threshold independent detection and localization of diffraction-limited spots.

Overview

In biomedical microscopy data, a common task involves the detection of diffraction-limited spots that visualize single proteins, domains, mRNAs, and many more. These spots were traditionally detected with mathematical operators such as Laplacian of Gaussian. These operators, however, rely on human input ranging from image-intensity thresholds, approximative spot sizes, etc. This process is tedious and not always reliable. DeepBlink relies on neural networks to automatically find spots without the need for human intervention. DeepBlink is available as a ready-to-use command-line interface.

Installation

pip install deepblink

You can also install the in-development version with:

pip install git+ssh://[e-mail]/bbquercus/deepblink/bbquercus/deepblink.git@master

Documentation

https://deepblink.readthedocs.io/

Development

To run the all tests run:

tox

Note, to combine the coverage data from all the tox environments run:

Windows	set PYTEST_ADDOPTS=--cov-append tox
Other	PYTEST_ADDOPTS=--cov-append tox

Changelog

0.0.4 (2020-07-10)

• Addition of command line interface (currently without verbosity capabilities).

• Bin/ folder with ready to use training script.

• Removal of src/ directory. Deepblink is now sailing GitHub on its own.

• Major docs overhaul with the addition of more detailed input / functionality descriptions and the addition of a usage overview and example in README.

• @zhanyinx is now listed as co-author.

0.0.3 (2020-07-02)

• First custom code release.

• All utility functions and training loop included.

• CLI still cookiecutter and not functional.

• First of five patches leading up to the first minor version:

  • v0.0.3 Utility functions.

  • v0.0.4 Command line interface for inference and script folder for training.

  • v0.0.5 Evaluation added to measure performance on test dataset.

  • v0.0.6 Addition of tests and completion of current TODO’s.

  • V0.0.7 Benchmarks/functions added to compare deepblink to other methods.

0.0.2 (2020-06-29)

• Still cookiecutter code but addition of docstrings to test sphinx apidoc capabilities.

0.0.1 (2020-06-24)

• First release on PyPI with cookiecutter HelloWorld template to set everything up.