The imagej.github.io from weisongzhao

Weisong Zhao, Ph.D.

Professor, PI, microscopist, and data scientist at Harbin Institute of Technology (HIT).
His research interest focuses on biomedical imaging, machine learning, and bioimage analysis.
His lab is building advanced optical microscopy for biomedical applications, as well as developing smart algorithms across modalities including optical microscopy, acoustic/photoacoustic imaging, and cryo-EM/ET.

2024-01: SN2N is fully open-source;
2022-10: PANELpy is fully open-source;
2022-05: SACDm and SACDj are fully open-source;
2021-11: A Python version with GPU accelartion of the Sparse deconvolution is released at sparse-deconv-py;
2021-11: I post a 'behind the paper' blog about the Sparse deconvolution at Nature Research Community;
2021-07: PANELM and PANELJ are fully open-source;
2021-03: An OPEN scientific discussion about deconvolution/sparse-deconvolution is posted on GitHub as well as on Twitter;
2020-11: Sparse-SIM is fully open-source!
2020-01: img2vid v0.1.0 released.
2020-01: Adaptive filter imagej-plugin v0.1.0 released.
2020-01: Sparse-SIM v1.0.3 released .p code.

Name	MATLAB	Java (ImageJ)	Python	Other languages	Reference	Description
SN2N	-	-	SN2N	-	bioRxiv	Self-inspired Noise2Noise learning to denoise engine
rFRC & PANEL	PANELM	PANELJ	PANELpy	-	Light: Sci. Appl.	Quantitatively mapping the local image quality at super-resolution scale
SACD	SACDm	SACDj	-	-	Nat. Photon.	100 times faster super-resolution fluctuation imaging.
Sparse deconvolution	Sparse-SIM	-	sparse-deconv-py	-	Nat. Biotech.	An universal post-processing framework for fluorescence microscopy.
ImagePy	-	-	ImagePy	-	Bioinformatics	An open source image processing framework (A Pythonic ImageJ).
Simulation for Adaptive Optics	Adaptive-Optics-simulation	-	-	-	Rev. Sci. Instrum.	A light weight simulation framework for adaptive optics in microscopy.
img2vid	img2vid	-	-	-	Nat. Biotech.	A light weight framework for making exsiting images to videos.
Palette.ui	Palette.ui	-	-	-	Nat. Biotech.	Multi-color imaging tool to merge/composite frames.
Adaptive median filter	-	Adaptive-Median-imagej	-	-	Nat. Biotech.	A median filter with adaptive threshold to avoid blurring effects.
t-varianceJ	-	t-varianceJ	-	-	-	T-axial variance calculation will highlight the regions that have calcium signal transients.
Clean Web Template	-	-	-	CleanWeb-Template (html/Javascript)	-	A light weight personal website template.