Official Python implementation of the 'Sparse deconvolution'-v0.3.0

Last update: Dec 28, 2022

Overview

Sparse deconvolution_{Python v0.3.0}

Official Python implementation of the 'Sparse deconvolution', and the CPU (NumPy) and GPU (CuPy) calculation backend will be automatically selected.

We haven’t tested it thoroughly, and the development is work in progress, so expect rough edges. As a result, feedback, questions, bug reports, and patches are welcome and encouraged!

It is a part of publication. For details, please refer to: "Weisong Zhao et al. Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy, Nature Biotechnology (2021)".

Instruction

NOTE: The MATLAB version and detailed information can be found at https://github.com/WeisongZhao/Sparse-SIM.
NOTE: The GPU acceleration feature using CuPy requires a CUDA-based NVIDIA GPU. It could provide a ~30 times faster reconstruction speed for a 512 × 512 × 5 image stack.
Clone/download, and run the demo.py

from sparse_recon.sparse_deconv import sparse_deconv

im = io.imread('test.tif')
plt.imshow(im,cmap = 'gray')
plt.show()

pixelsize = 65 #(nm)
resolution = 280 #(nm)

img_recon = sparse_deconv(im, resolution / pixelsize)
plt.imshow(img_recon / img_recon.max() * 255,cmap = 'gray')
plt.show()

Tested dependency

Python 3.7
NumPy 1.21.4
CuPy 9.6.0 (CUDA 11.5)
PyWavelets 1.1.1

Version

v0.3.0 full Sparse deconvolution features
v0.2.0 iterative deconvolution
v0.1.0 initialized and started from dzh929

Open source Sparse deconvolution

This software and corresponding methods can only be used for non-commercial use, and they are under Open Data Commons Open Database License v1.0.
Feedback, questions, bug reports and patches are welcome and encouraged!

Official Python implementation of the 'Sparse deconvolution'-v0.3.0

Related tags

Overview

Sparse deconvolution_{Python v0.3.0}

Instruction

Tested dependency

Version

Related links: img2vid, Adaptive filter imagej-plugin, and Merge channels

Open source Sparse deconvolution

Owner

Weisong Zhao

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Official Python implementation of the 'Sparse deconvolution'-v0.3.0

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Instruction

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Owner

Weisong Zhao

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Sparse deconvolution_{Python v0.3.0}