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    19 repositories

    • siMILe

      Public
      GNU Affero General Public License v3.0
      •0•0•1•0•Updated Apr 3, 2026Apr 3, 2026

    • nERdy

      Public
      nERdy: network analysis of ER dynamics
      Python
      •
      GNU Affero General Public License v3.0
      •1•2•0•1•Updated Jan 29, 2026Jan 29, 2026

    • .github

      Public
      TeX
      •
      GNU Affero General Public License v3.0
      •3•0•2•0•Updated Dec 18, 2025Dec 18, 2025

    • tutorial_mcs_detect

      Public
      Run ER-Mitochondria contact detection in 5 minutes or less.
      Shell
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Mar 2, 2025Mar 2, 2025

    • SubPrecisionContactDetection.jl

      Public
      A Julia package to detect contacts below the precision of a superresolution microscope between 2 subcellular organelles in 2-channel superresolution (STED) mic…
      Julia
      •
      GNU Affero General Public License v3.0
      •0•0•1•0•Updated Sep 19, 2024Sep 19, 2024

    • NanoscopyAi_Webpage

      Public
      0•0•0•0•Updated May 21, 2024May 21, 2024

    • projectemplate

      Public
      A research project template outlining the scope, proposed research question, related work, data, needed for a research project
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated May 15, 2024May 15, 2024

    • autophagy_example

      Public
      An example of using SPECHT.jl for autophagy in confocal microscopy
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated May 14, 2024May 14, 2024

    • tutorial_smlm_alignment_colocalization

      Public
      Tutorial on how to process large datasets of SMLM data (point cloud/dSTORM). Includes fiducial tracking, alignment, then colocalization.
      ImageJ Macro
      •
      GNU Affero General Public License v3.0
      •1•0•1•0•Updated Apr 15, 2024Apr 15, 2024

    • icons

      Public
      Public repository for hosting icons used for web access without authentication.
      0•0•0•0•Updated Mar 7, 2024Mar 7, 2024

    • SmlmTools.jl

      Public
      Computational tools for single molecule localization / superresolution microscopy (point clouds). Mirror of https://github.com/bencardoen/SmlmTools.jl
      Julia
      •
      Other
      •0•0•0•0•Updated Jun 12, 2023Jun 12, 2023

    • Colocalization.jl

      Public
      Reference implementation of colocalization metrics. Mirror of https://github.com/bencardoen/Colocalization.jl
      Julia
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jun 12, 2023Jun 12, 2023

    • DataCurator.jl

      Public
      A scalable Julia package to transparently validate and transform large biomedical datasets using human readable recipes that are translated to machine verifiab…
      Julia
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jun 12, 2023Jun 12, 2023

    • cluster-tips

      Public
      A set of tips and trick for efficient cluster usage
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated May 25, 2023May 25, 2023

    • globus

      Public
      walkthrough on using Globus to efficiently access large datasets
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Mar 12, 2023Mar 12, 2023

    • repositorytemplate

      Public template
      A template for new project repositories
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Feb 27, 2023Feb 27, 2023

    • SPECHT.jl

      Public
      SPECHT is a Julia implementation of a contrastive weakly supervised object detection and identification method for fluorescence microscopy. Mirror of https://…
      Julia
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Feb 24, 2023Feb 24, 2023

    • ERGO

      Public
      ERGO: Efficient Recurrent Graph Optimized Emitter Density Estimation in Single Molecule Localization Microscopy. Mirror of https://github.com/bencardoen/ERGO
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Feb 24, 2023Feb 24, 2023

    • smlmvis

      Public
      Data loaders and visualization of 3D protein localization data from a range of superresolution microscopes. Mirror of https://github.com/bencardoen/smlmvis
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 24, 2023Feb 24, 2023
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