HUANG GROUP @ PURDUE
  • Home
  • News
  • PUBLICATIONS
  • Positions Available
  • Lab Members
  • Software
  • Contact
INSPR: in situ Point Spread Function Retrieval
INSPR toolbox is developed for both biplane and astigmatism-based setups. It constructs an in situ 3D point spread function (PSF) directly from the obtained single molecule dataset and features an easy-to-use user interface including all steps of 3D single molecule localization from INSPR model generation, pupil-based 3D localization (supporting both GPU with cubic spline implementation and CPU versions), drift correction, volume alignment, to super-resolution image reconstruction. It also contains a small single molecule dataset for users to run as an example.

Full Reference: Fan Xu, Donghan Ma, Kathryn P. MacPherson, Sheng Liu, Ye Bu, Yu Wang, Yu Tang, Cheng Bi, Tim Kwok, Alexander A. Chubykin, Peng Yin, Sarah Calve, Gary E. Landreth, and Fang Huang, "Three-dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval" (2020) Nature Methods, 17(5): 531-540.
Picture
Available in Github at:
https://github.com/HuanglabPurdue/INSPR
coded in: 
MATLAB
CUDA
Download
Fork
Follow @HuanglabPurdue

Contributors:
Fan Xu (xu240@purdue.edu)
Sheng Liu (liu1840@purdue.edu)
NCS: Noise Correction Algorithm for sCMOS Cameras
NCS (noise correction algorithm for sCMOS (CMOS) cameras) is an algorithm that minimizes sCMOS noise (termed 'pixel-dependent noise') from microscopy images with arbitrary structures. ​

Full Reference: S. Liu, M. J. Mlodzianoski, Z. Hu, Y. Ren, K. McElmurry, D. M. Suter, F. Huang, "sCMOS noise-correction algorithm for microscopy images" (2017) Nature Methods, Vol. 14, 8, 760 - 761.
Picture
Available in Github at:
​​https://github.com/HuanglabPurdue/NCS
coded in: 
MATLAB
​Python 3.6
Download
Fork
Follow @HuanglabPurdue

Contributors:
Sheng Liu (liu1840@purdue.edu)
David Miller (davidmiller2023.1@u.northwestern.edu)
Ben Brenner (​bbrenne@purdue.edu)
Simplex AO: Simplex Algorithm based Adaptive Optics in Single Molecule Switching Nanoscopy
This package contains an example labview code module for implementing Nelder-Mead Simplex Algorithm for AO and adaptive PSF shaping in SMSN.

Big thanks for Edward Allgeyer and George Sirinakis, University of Cambridge for programming parts of subvis included in this module

​Full Reference: M. J. Mlodzianoski, P. J. Cheng-Hathaway, S. M. Bemiller, T. J. McCray, S. Liu, D. A. Miller, B. T. Lamb, G. E. Landreth, F. Huang, "Active PSF shaping and adaptive optics enable volumetric localization microscopy through brain sections" (2018) Nature Methods, Advance Online Publication, doi: 10.1038/s41592-018-0053-8​​
Picture
Available in Github at:
https://github.com/HuanglabPurdue/AO_SMSN
coded in: 
LabView
Download
Fork
Follow @HuanglabPurdue

Contributors: 
​
Michael Mlodzianoski (michael.mlodzianoski@gmail.com)
smNet: Deep Neural Network for Single Molecule and Super-Resolution Imaging
smNet: a deep neural network to retrieve multiple classes of information from single molecule emission patterns with precision approaching the theoretical limit.

PSF Toolbox: Pupil based PSF generator 

​Full Reference: P. Zhang*, S. Liu*, A. Chaurasia, D. Ma, M. J. Mlodzianoski, E. Culurciello and F. Huang, "Analyzing complex single molecule emission patterns with deep learning"(2018) Nature Methods, doi: https://doi.org/10.1038/s41592-018-0153-5, *Equal Contribution
Picture
Available in Github at:
https://github.com/HuanglabPurdue/smNet
coded in: 
LuaJIT
Torch
​MATLAB
Download
Fork
Follow @HuanglabPurdue

Contributors:
Peiyi Zhang (zhan2653@purdue.edu)
Sheng Liu (liu1840@purdue.edu)
Purdue University, Weldon School of Biomedical Engineering, Martin C. Jischke Hall of Biomedical Engineering
206 S. Martin Jischke Drive, West Lafayette, IN 47907-2032
  • Home
  • News
  • PUBLICATIONS
  • Positions Available
  • Lab Members
  • Software
  • Contact