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

Overview

paper Github commit License
Twitter GitHub watchers GitHub stars GitHub forks

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

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

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!
Owner
Weisong Zhao
I'm currently a Ph.D. student at Harbin Institute of Technology.
Weisong Zhao
Generating Digital Painting Lighting Effects via RGB-space Geometry (SIGGRAPH2020/TOG2020)

Project PaintingLight PaintingLight is a project conducted by the Style2Paints team, aimed at finding a method to manipulate the illumination in digit

651 Dec 29, 2022
ADGAN - The Implementation of paper Controllable Person Image Synthesis with Attribute-Decomposed GAN

ADGAN - The Implementation of paper Controllable Person Image Synthesis with Attribute-Decomposed GAN CVPR 2020 (Oral); Pose and Appearance Attributes Transfer;

Men Yifang 400 Dec 29, 2022
Gender Classification Machine Learning Model using Sk-learn in Python with 97%+ accuracy and deployment

Gender-classification This is a ML model to classify Male and Females using some physical characterstics Data. Python Libraries like Pandas,Numpy and

Aryan raj 11 Oct 16, 2022
A Pytree Module system for Deep Learning in JAX

Treex A Pytree-based Module system for Deep Learning in JAX Intuitive: Modules are simple Python objects that respect Object-Oriented semantics and sh

Cristian Garcia 216 Dec 20, 2022
This repository provides an unified frameworks to train and test the state-of-the-art few-shot font generation (FFG) models.

FFG-benchmarks This repository provides an unified frameworks to train and test the state-of-the-art few-shot font generation (FFG) models. What is Fe

Clova AI Research 101 Dec 27, 2022
Official repository for Automated Learning Rate Scheduler for Large-Batch Training (8th ICML Workshop on AutoML)

Automated Learning Rate Scheduler for Large-Batch Training The official repository for Automated Learning Rate Scheduler for Large-Batch Training (8th

Kakao Brain 35 Jan 04, 2023
Source code for "UniRE: A Unified Label Space for Entity Relation Extraction.", ACL2021.

UniRE Source code for "UniRE: A Unified Label Space for Entity Relation Extraction.", ACL2021. Requirements python: 3.7.6 pytorch: 1.8.1 transformers:

Wang Yijun 109 Nov 29, 2022
A simple, fast, and efficient object detector without FPN

You Only Look One-level Feature (YOLOF), CVPR2021 A simple, fast, and efficient object detector without FPN. This repo provides an implementation for

789 Jan 09, 2023
This repository contains the code for the paper in EMNLP 2021: "HRKD: Hierarchical Relational Knowledge Distillation for Cross-domain Language Model Compression".

HRKD: Hierarchical Relational Knowledge Distillation for Cross-domain Language Model Compression This repository contains the code for the paper in EM

Chenhe Dong 2 Mar 24, 2022
StyleGAN2-ADA-training-jupyter - Training custom datasets in styleGAN2-ADA by NVIDIA using Jupyter

styleGAN2-ADA-training-jupyter Training custom datasets in styleGAN2-ADA on Jupyter Official StyleGAN2-ADA by NIVIDIA Paper Training Generative Advers

Mang Su Hyun 2 Feb 24, 2022
FinGAT: A Financial Graph Attention Networkto Recommend Top-K Profitable Stocks

FinGAT: A Financial Graph Attention Networkto Recommend Top-K Profitable Stocks This is our implementation for the paper: FinGAT: A Financial Graph At

Yu-Che Tsai 64 Dec 13, 2022
Official implementation of "Not only Look, but also Listen: Learning Multimodal Violence Detection under Weak Supervision" ECCV2020

XDVioDet Official implementation of "Not only Look, but also Listen: Learning Multimodal Violence Detection under Weak Supervision" ECCV2020. The proj

peng 64 Dec 12, 2022
Self-supervised Label Augmentation via Input Transformations (ICML 2020)

Self-supervised Label Augmentation via Input Transformations Authors: Hankook Lee, Sung Ju Hwang, Jinwoo Shin (KAIST) Accepted to ICML 2020 Install de

hankook 96 Dec 29, 2022
Self-supervised learning algorithms provide a way to train Deep Neural Networks in an unsupervised way using contrastive losses

Self-supervised learning Self-supervised learning algorithms provide a way to train Deep Neural Networks in an unsupervised way using contrastive loss

Arijit Das 2 Mar 26, 2022
Enhancing Knowledge Tracing via Adversarial Training

Enhancing Knowledge Tracing via Adversarial Training This repository contains source code for the paper "Enhancing Knowledge Tracing via Adversarial T

Xiaopeng Guo 14 Oct 24, 2022
Repository for open research on optimizers.

Open Optimizers Repository for open research on optimizers. This is a test in sharing research/exploration as it happens. If you use anything from thi

Ariel Ekgren 6 Jun 24, 2022
Code for EMNLP 2021 main conference paper "Text AutoAugment: Learning Compositional Augmentation Policy for Text Classification"

Text-AutoAugment (TAA) This repository contains the code for our paper Text AutoAugment: Learning Compositional Augmentation Policy for Text Classific

LancoPKU 105 Jan 03, 2023
Code for the paper "Learning-Augmented Algorithms for Online Steiner Tree"

Learning-Augmented Algorithms for Online Steiner Tree This is the code for the paper "Learning-Augmented Algorithms for Online Steiner Tree". Requirem

0 Dec 09, 2021
A clean and robust Pytorch implementation of PPO on continuous action space.

PPO-Continuous-Pytorch I found the current implementation of PPO on continuous action space is whether somewhat complicated or not stable. And this is

XinJingHao 56 Dec 16, 2022
TSDF++: A Multi-Object Formulation for Dynamic Object Tracking and Reconstruction

TSDF++: A Multi-Object Formulation for Dynamic Object Tracking and Reconstruction TSDF++ is a novel multi-object TSDF formulation that can encode mult

ETHZ ASL 130 Dec 29, 2022