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    25 repositories

    • Sabate_et_al_TAD_Anchors

      Public
      Python scripts to analyze loop extrusion from microscopy images and simulations
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 2, 2025Nov 2, 2025

    • comcortxt

      Public
      comcor study, free text analysis
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 17, 2025Jun 17, 2025

    • shareloc-collection

      Public
      RDF Collection for ShareLoc.XYZ
      Python
      •0•2•0•1•Updated May 15, 2025May 15, 2025

    • ShareLoc.XYZ

      Public
      A platform for sharing localization microscopy data.
      JavaScript
      •
      MIT License
      •2•4•16•16•Updated Feb 27, 2025Feb 27, 2025

    • Brightfield-Drift-Correction-3D

      Public
      Acquire bright field images along with the super resolution data and use it to track drift in 3D with nanometer precision!
      localizationtracedrift
      localizationtracedriftmicroscopycross-correlationbrighfield
      Python
      •
      MIT License
      •0•11•1•0•Updated Jun 22, 2023Jun 22, 2023

    • ANNA-PALM

      Public
      Accelerating Single Molecule Localization Microscopy with Deep Learning
      Python
      •
      Other
      •14•53•12•2•Updated Mar 24, 2023Mar 24, 2023

    • shareloc-utils

      Public
      Utility tools for ShareLoc.XYZ
      Python
      •
      MIT License
      •0•0•1•18•Updated Mar 6, 2023Mar 6, 2023

    • LoopExtrusion

      Public
      A tool to simulate loop extrusion in chromatin
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 11, 2023Jan 11, 2023

    • smlm-file-format

      Public
      A portable and extendable file format for storing and sharing localization microscopy data.
      Java
      •
      MIT License
      •2•6•0•1•Updated Oct 6, 2022Oct 6, 2022

    • ZOLA-3D

      Public
      Zernike Optimized Localization Algorithm for 3D single molecule localizations
      Java
      •
      GNU General Public License v3.0
      •3•19•4•0•Updated Sep 20, 2022Sep 20, 2022

    • smlm-viewer

      Public
      JavaScript
      •0•0•0•0•Updated Aug 4, 2021Aug 4, 2021

    • Anet-ImageJ

      Public
      An ImageJ/FIJI plugin for running Anet, for processing images with ANNA-PALM and other models in ImageJ/FIJI.
      Java
      •
      GNU General Public License v3.0
      •1•5•0•0•Updated Apr 16, 2021Apr 16, 2021

    • VoroQuant

      Public
      A 3D-voronoi-based python program to quantify SMLM data
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 25, 2021Mar 25, 2021

    • ArduinoCompressedSensing

      Public
      A compressed sensing plugin for MicroManager to perform compressed sensing acquisitions
      C++
      •0•2•0•0•Updated Apr 9, 2017Apr 9, 2017

    • pySPIRALTAP

      Public
      Sparse Poisson Intensity Reconstruction ALgorithms
      Jupyter Notebook
      •
      MIT License
      •5•8•1•0•Updated Apr 2, 2017Apr 2, 2017

    • CompressedSensingMicroscopy3D

      Public
      Reconstruction notebooks for the paper "Simple 3D compressed sensing scheme for faster and less phototoxic fluorescence microscopy imaging"
      Jupyter Notebook
      •1•7•0•0•Updated Apr 2, 2017Apr 2, 2017

    • lutorpy

      Public
      Use torch in python for deep learning.
      Python
      •
      MIT License
      •140•233•21•0•Updated Feb 9, 2017Feb 9, 2017

    • DeepCell

      Public
      Python
      •24•0•0•0•Updated Nov 5, 2016Nov 5, 2016

    • keras

      Public
      Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano and TensorFlow.
      Python
      •
      Other
      •20k•7•0•0•Updated Nov 4, 2016Nov 4, 2016

    • TaggedSpot2CSV

      Public
      Convert Tagged Spot File (.tsf from MicroManager) to Comma Separated Values file(.csv for thunderSTORM)
      Protocol Buffer
      •
      MIT License
      •0•0•0•0•Updated Oct 2, 2016Oct 2, 2016

    • mnist-deep-learning-tutorial

      Public
      Jupyter Notebook
      •1•2•0•0•Updated Sep 29, 2016Sep 29, 2016

    • RNNtrajAnalysis

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Sep 29, 2016Sep 29, 2016

    • thunderstorm

      Public
      ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging
      Java
      •
      GNU General Public License v3.0
      •44•0•0•0•Updated Mar 4, 2016Mar 4, 2016

    • sagenb

      Public
      Sage Notebook for super-resolution imaging automation
      JavaScript
      •
      Other
      •96•1•10•0•Updated Mar 10, 2015Mar 10, 2015

    • QuickPALM

      Public
      A 3D real-time PALM/STORM image processing plugin for ImageJ
      Java
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Feb 3, 2015Feb 3, 2015
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