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@znamlab Znamenskiy lab

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    40 repositories

    • 2p-preprocess

      Public
      Tools for preprocessing 2p calcium imaging data
      Python
      •1•3•4•0•Updated Apr 24, 2026Apr 24, 2026

    • cottage_analysis

      Public
      Potentially temporary repository to use DLC to track eye position
      Python
      •
      MIT License
      •1•0•8•1•Updated Apr 20, 2026Apr 20, 2026

    • v1_depth_map

      Public
      Analysis code for 2p imaging for 3d vision project
      Jupyter Notebook
      •0•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • tile_picker

      Public
      GUI for selecting tiles for imaging on the ISS microscope
      Python
      •0•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • flexiznam

      Public
      Znam lab tool to interact with flexilims
      Python
      •
      MIT License
      •0•0•13•0•Updated Apr 13, 2026Apr 13, 2026

    • python-cookiecutter

      Public
      Utility to create a basic Python project structure with tests, CI etc.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•0•0•0•Updated Apr 12, 2026Apr 12, 2026

    • brisc

      Public
      Barcoded Rabies In Situ Connectomics
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 11, 2026Apr 11, 2026

    • iss-preprocess

      Public
      Utilities for image import, registration, puncta localisation and base-calling for ISS data sets
      Python
      •
      MIT License
      •0•1•16•0•Updated Mar 19, 2026Mar 19, 2026

    • ROICaT

      Public
      Region Of Interest Classification and Tracking
      Python
      •
      GNU General Public License v3.0
      •12•0•0•0•Updated Mar 16, 2026Mar 16, 2026

    • aind-ephys-preprocessing

      Public
      CodeOcean capsule for ephys preprocessing
      Python
      •
      MIT License
      •2•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • spikeinterface

      Public
      A Python-based module for creating flexible and robust spike sorting pipelines.
      Python
      •
      MIT License
      •259•0•0•0•Updated Feb 13, 2026Feb 13, 2026

    • znamlab.github.io

      Public
      Znamenskiy lab website
      SCSS
      •
      MIT License
      •3•0•0•2•Updated Feb 10, 2026Feb 10, 2026

    • aind-ephys-curation

      Public
      Code Ocean capsule for ephys curation
      Python
      •
      MIT License
      •5•0•0•0•Updated Feb 9, 2026Feb 9, 2026

    • aind-ephys-visualization

      Public
      CodeOcean capsule for ephys visualization
      Python
      •
      MIT License
      •2•0•0•0•Updated Feb 9, 2026Feb 9, 2026

    • harp-python

      Public
      A low-level interface to data collected with the Harp binary protocol
      Python
      •
      MIT License
      •5•0•0•0•Updated Jan 12, 2026Jan 12, 2026

    • multi_padlock_design

      Public
      Padlock design tool modified for running on slurm
      Python
      •
      MIT License
      •0•3•1•1•Updated Dec 23, 2025Dec 23, 2025

    • iss-analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 19, 2025Dec 19, 2025

    • senses-in-motion

      Public
      Senses in Motion Symposium website
      SCSS
      •
      MIT License
      •1•0•0•0•Updated Dec 8, 2025Dec 8, 2025

    • flexilims

      Public
      Python wrappers around the flexilims API
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 17, 2025Nov 17, 2025

    • suite2p

      Public
      cell detection in calcium imaging recordings
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •271•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • image-tools

      Public
      Simple utilities to work with images
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • znamutils

      Public
      Common utility functions for Znamenskiy's lab projects
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 8, 2025Sep 8, 2025

    • MAPseq_processing

      Public
      Pipeline for processing MAPseq NGS datasets
      Python
      •0•0•0•0•Updated Jul 27, 2025Jul 27, 2025

    • cricksaw-analysis

      Public
      Postprocessing and analysis of Cricksaw data
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 17, 2025Jul 17, 2025

    • ccf_streamlines

      Public
      This package supports projection of Common Cortical Framework (CCF) volumetric data and coordinate data on to flattened representations.
      Python
      •
      Other
      •1•0•0•0•Updated Jun 6, 2025Jun 6, 2025

    • vis-stim-depth

      Public
      Codes for visual stimulation for depth mapping
      C#
      •0•2•3•0•Updated Apr 1, 2025Apr 1, 2025

    • wayla

      Public
      What are you looking at? A gaze reconstruction package for mice.
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 27, 2024Sep 27, 2024

    • bg-atlasapi

      Public
      A lightweight python module to interact with atlases for systems neuroscience
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •65•0•0•0•Updated Jul 24, 2024Jul 24, 2024

    • pymcms

      Public
      Wrapper to interact with MCMS API
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 16, 2024Jan 16, 2024

    • TIFFStack

      Public
      Load TIFF files into matlab fast, with lazy loading
      MATLAB
      •
      Other
      •20•0•0•0•Updated May 3, 2023May 3, 2023
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