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@BIIFSweden SciLifeLab BioImage Informatics Facility

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    40 repositories

    • Webinar_ImageRegistration_Mar2026

      Public
      It contains the Jupyter Notebook that was used during the webinar demonstration and the presentation slides
      Jupyter Notebook
      •0•1•0•0•Updated Apr 9, 2026Apr 9, 2026

    • BIIFSweden.github.io

      Public
      Webpage for BIIF's project's list
      0•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • ChristelBergstrom2024-1

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

    • DropletHR

      Public
      Droplet Microfluidics for detection of bacterial heteroresistance
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • 6870_isPLA

      Public
      Spatial Proteomics: In Situ PLA data
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 10, 2025Nov 10, 2025

    • 8134_amyloid_formation

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

    • LCI_Workshop

      Public
      Image Analysis workshop of the LCI Microscopy course
      ImageJ Macro
      •
      MIT License
      •3•1•0•0•Updated Aug 7, 2025Aug 7, 2025

    • pipex_bigfish

      Public
      A pipeline to transform images into valuable analysis items
      Python
      •
      MIT License
      •2•0•0•0•Updated Jun 9, 2025Jun 9, 2025

    • SLU2025-AI4BIA

      Public
      Lecture material for "AI tools in biology" at SLU 2025: "AI and image analysis"
      0•0•0•0•Updated Feb 18, 2025Feb 18, 2025

    • I2K2024-MTIWorkshop

      Public
      Material for the I2K 2024 "Multiplexed tissue imaging: tools and approaches" workshop
      Jupyter Notebook
      •1•5•0•0•Updated Oct 23, 2024Oct 23, 2024

    • quantMSImageR

      Public
      Extensions to cardinal for quantitative mass spectrometry imaging.
      R
      •
      GNU General Public License v3.0
      •1•0•0•1•Updated Oct 5, 2024Oct 5, 2024

    • spermatogenesis-profiling

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•1•0•Updated Sep 19, 2024Sep 19, 2024

    • GFP-LC3-dot-counting

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 11, 2024Mar 11, 2024

    • birka

      Public
      A tool for bioimage data validation and archival
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Feb 13, 2024Feb 13, 2024

    • birka-installer

      Public
      Installer for Birka, the BioImage Archiver
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 12, 2024Feb 12, 2024

    • staged-recipes

      Public
      A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5.9k•0•0•0•Updated Feb 9, 2024Feb 9, 2024

    • CellGeometryProfiling

      Public
      Cell's geometry profiling for neonatal rat cardiomyocytes in 2D culture
      ImageJ Macro
      •
      MIT License
      •0•1•0•0•Updated Feb 7, 2024Feb 7, 2024

    • GoranJonsson2024-1

      Public
      Run GPU-enabled containers for Jupyter Lab and QuPath using Podman
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated Jan 18, 2024Jan 18, 2024

    • jupyter-xprahtml5-proxy

      Public
      Jupyter extensions for running a Xpra Session proxy
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•0•0•0•Updated Dec 14, 2023Dec 14, 2023

    • mm-fft-example

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 7, 2023Dec 7, 2023

    • EduardoVillablanca2023-1

      Public
      Segmentation of ducts in histology tissue using the NoCodeSeg pipeline
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Dec 1, 2023Dec 1, 2023

    • SenolyticDetection

      Public
      Senescent Analysis.
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 11, 2023Oct 11, 2023

    • cookiecutter-analysis-macros

      Public
      A cookiecutter template for macro-based image analysis projects conducted by the SciLifeLab BioImage Informatics Facility (BIIF)
      Python
      •2•0•0•1•Updated Sep 28, 2023Sep 28, 2023

    • cookiecutter-analysis-python

      Public
      A cookiecutter template for Python-based image analysis projects conducted by the SciLifeLab BioImage Informatics Facility (BIIF)
      Python
      •2•1•0•0•Updated Sep 28, 2023Sep 28, 2023

    • cookiecutter-analysis

      Public
      A cookiecutter template for image analysis projects conducted by the SciLifeLab BioImage Informatics Facility (BIIF)
      Python
      •2•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • EpithelialNetworkAnalysis

      Public
      ImageJ Macro
      •
      MIT License
      •0•0•0•0•Updated Sep 21, 2023Sep 21, 2023

    • CoregistrationMultiplexed

      Public
      Python
      •
      MIT License
      •0•3•0•0•Updated Sep 14, 2023Sep 14, 2023

    • CellTypeAnalysis

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Aug 28, 2023Aug 28, 2023

    • Lund_Multiplexed

      Public
      Course on using QuPath for multiplexed data
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 12, 2023Jul 12, 2023

    • docs

      Public
      Internal BIIF documentation
      0•0•0•0•Updated Jul 3, 2023Jul 3, 2023
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