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    36 repositories

    • multicelldetection

      Public
      Multi-cell Detection for Confocal Images of the embryo of Xenopus laevis tadpoles
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • Galaxy_workflow_bulk_RNA-seq-

      Public
      Galaxy tools needed to run Thomas Vannier's differential expression workflow on Galaxy
      R
      •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • AFM-leveling

      Public
      Python scripts for AFM data processing and analysis
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • Software_Python_OpenLabFram

      Public
      Python
      •1•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • ProtruDe

      Public
      Repository of ImageJ macros and plugins for detecting protrusion in the videos of SARS-CoV-2 spike protein, captured by high-speed atomic force microscope.
      Java
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 6, 2024Mar 6, 2024

    • differential-expression_workflow

      Public
      This workflow performs an RNA-seq analysis from the sequencing output data to the differential expression analyses.
      bulk-rna-seqrna-seq-analysis
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Nov 16, 2023Nov 16, 2023

    • cataloger

      Public
      Filling form for microscopy image annotations (on the biology side of things)
      omero-import
      Python
      •
      MIT License
      •0•2•7•1•Updated Jun 9, 2023Jun 9, 2023

    • clicket

      Public archive
      Adaptation of https://github.com/evereux/flicket app to suit our needs
      Python
      •
      MIT License
      •0•0•3•2•Updated May 1, 2023May 1, 2023

    • Microbiome-Analysis-Workflow

      Public
      This workflow performs a metabarcoding analysis from the reads sequencing to the production of a report presenting the graphical results.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Dec 8, 2022Dec 8, 2022

    • metrologist

      Public archive
      Python
      •
      MIT License
      •2•0•1•4•Updated Sep 12, 2022Sep 12, 2022

    • motorized-stereotaxic-arm

      Public
      C++
      •1•0•0•0•Updated Sep 7, 2022Sep 7, 2022

    • metatranscriptomics-bulkrnaseq_workflow

      Public
      This workflow performs a metatranscriptomics and bulk RNAseq analysis from the sequencing output data to the differential expression analyses.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Jul 27, 2022Jul 27, 2022

    • AdoptOmero

      Public
      Makefile
      •0•0•0•0•Updated Jun 28, 2022Jun 28, 2022

    • syringe_drivers

      Public
      C++
      •
      Mozilla Public License 2.0
      •2•1•0•0•Updated Apr 22, 2022Apr 22, 2022

    • BD_BlobsSeg

      Public
      Fiji macro to segment blobs-like organelles
      ImageJ Macro
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 14, 2022Apr 14, 2022

    • 3D-ImageJ-Suite

      Public
      0•0•0•0•Updated Feb 25, 2022Feb 25, 2022

    • scRNAseq_analysis_workflow

      Public
      Single-Cell RNA-seq analysis workflow for 10x Genomics data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Jan 21, 2022Jan 21, 2022

    • napari-openlabframe

      Public
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 14, 2021Dec 14, 2021

    • olf_control

      Public
      Python
      •
      Other
      •0•1•0•0•Updated Dec 14, 2021Dec 14, 2021

    • omero-at-centuri

      Public
      Shell
      •0•0•0•0•Updated Sep 30, 2021Sep 30, 2021

    • impomero

      Public
      Omero auto importer
      omero-import
      Python
      •0•2•2•0•Updated Sep 24, 2021Sep 24, 2021

    • auto_metro

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Sep 8, 2021Sep 8, 2021

    • BD_EpiCellSeg

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 17, 2021Jun 17, 2021

    • BioimageDatabaseCourse

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Jun 8, 2021Jun 8, 2021

    • wiki

      Public
      our wiki
      0•0•1•0•Updated Jun 7, 2021Jun 7, 2021

    • ply-zarr

      Public
      A zarr implementation of the PLY specification
      Python
      •0•1•0•0•Updated May 6, 2021May 6, 2021

    • optoPlate-96

      Public
      All design files and scripts necessary for the construction and use of the optoPlate-96
      C++
      •3•0•0•0•Updated May 3, 2021May 3, 2021

    • flask-video-streaming

      Public
      Supporting code for my article on video streaming with Flask.
      Python
      •
      MIT License
      •526•0•0•0•Updated Mar 19, 2021Mar 19, 2021

    • jolo

      Public
      Jupyter / voilà interface to OLOGRAM
      Python
      •
      GNU General Public License v3.0
      •0•0•2•0•Updated Feb 22, 2021Feb 22, 2021

    • primer_deeplearning

      Public
      some basics and tips for starting a DL project
      0•0•0•0•Updated Feb 22, 2021Feb 22, 2021