Repositories list

• MERlin

  Public
  MERFISH decoding software

  Python

  •

  MIT License

  •31•26•0•0•Updated Aug 16, 2025Aug 16, 2025

• storm-control

  Public
  Microscope control software

  Python

  •

  Other

  •70•68•17•1•Updated Feb 13, 2025Feb 13, 2025

• Chromatin_Analysis_MOp

  Public
  Analysis codes and scripts for chromatin of MOp

  Jupyter Notebook

  •

  MIT License

  •2•3•1•0•Updated Jan 11, 2025Jan 11, 2025

• whole_mouse_brain_MERFISH_atlas_scripts_2023

  Public
  Jupyter Notebook

  •6•8•1•0•Updated Mar 29, 2024Mar 29, 2024

• storm-analysis

  Public
  STORM movie analysis code

  Python

  •91•121•3•1•Updated Feb 23, 2024Feb 23, 2024

• SpatialBrainAgingCell22

  Public
  Jupyter Notebook

  •4•13•0•0•Updated Dec 19, 2022Dec 19, 2022

• Epigenomic_MERFISH

  Public
  MATLAB

  •0•2•0•0•Updated Oct 21, 2022Oct 21, 2022

• Chromatin_Analysis_2020_cell

  Public
  Source codes and example scripts for chromatin tracing projects in Zhuang lab

  Jupyter Notebook

  •

  MIT License

  •8•27•3•0•Updated Jan 27, 2022Jan 27, 2022

• MERFISH_analysis

  Public
  Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.

  MATLAB

  •

  Other

  •32•50•4•1•Updated Aug 1, 2021Aug 1, 2021

• BICCN_MOp_2021

  Public
  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Apr 28, 2021Apr 28, 2021

• 3D-printing

  Public
  Designs for 3D printed parts that were developed in the Zhuang Lab.

  OpenSCAD

  •4•11•0•0•Updated Dec 2, 2020Dec 2, 2020

• matlab-storm

  Public
  GUIs and functions for analyzing STORM data in MATLAB

  MATLAB

  •61•40•5•0•Updated May 22, 2020May 22, 2020

• MERFISH-based-CRISPR-screening

  Public
  Software for high-throughput, MERFISH-based CRISPR screening.

  MATLAB

  •0•0•0•0•Updated May 6, 2019May 6, 2019

• MERFISH-based-screening

  Public
  Software for high-throughput, image-based screening using MERFISH.

  Python

  •0•0•0•0•Updated Oct 30, 2017Oct 30, 2017