This codec is designed for compressing movies with Poisson noise, which are produced by photon-limited modalities such multiphoton microscopy, radiography, and astronomy.
The codec assumes that the video is linearly encoded with a potential offset (zero_level) and that the photon_sensitivity (the average increase in intensity per photon) is known or can be accurately estimated from the data.
The codec re-quantizes the grayscale efficiently with a square-root-like transformation to equalize the noise variance across the grayscale levels: the Anscombe Transform. This results in a smaller number of unique grayscale levels and significant improvements in the compressibility of the data without sacrificing signal accuracy.
To use the codec, one must supply two pieces of information: zero_level (the input value corresponding to the absence of light) and photon_sensitivity (levels/photon).
The codec is used in Zarr as a filter prior to compression.
Zarr.
Install via pip:
pip install poisson-numcodecs
conda create -n poisson_numcodecs python=3.xx
conda activate poisson_numcodecs
git clone https://github.com/AllenNeuralDynamics/poisson-numcodecs.git
cd poisson-numcodecs
pip install -r requirements.txt
pip install -e .
Make sure everything works:
pip install pytest
pytest tests/
An complete example is provided in examples/workbook.ipynb