The Nextflow Podcast

Episode 39: Spatial proteomics at Pixelgen

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Tune in to hear all about Pixelgen Technologies - creators of a novel technology

for doing single-cell spatial proteomics.


We chat about how this fascinating technology works, what you can do with the data

and why they chose to develop their analysis suite as an open-source nf-core pipeline.


Links:

  • Software:
    • nf-core/pixelator pipeline
    • Pixelator Python package
    • Science:
      • Nature Methods publication: “Molecular pixelation: spatial proteomics of single cells by sequencing”
      • Presentations:
        • Nextflow Summit 2022 talk: “Pixelgen Technologies ❤︎ Nextflow”
        • Nextflow Summit 2024 Boston talk: “Nextflow allows Pixelgen innovation engine to reach the market quicker”
        • Nextflow Summit 2024 Barcelona
        • Pixelgen:
          • Pixelgen Technologies homepage
          • @PixelgenTech on twitter / X and LinkedIn
          • BioLizard:
            • BioLizard homepage
            • @BioLizard_nv on twitter / X and LinkedIn


              • Chapters:

              • Start (00:00)
              • Welcome (00:09)
              • Introductions (00:50)
              • Intro to Pixelgen Technologies (01:41)
              • Lab methods (03:08)
              • Nature Methods publication (06:15)
              • Data visualisation (09:35)
              • Working with single cell data (12:29)
              • Cell interactions (15:06)
              • Why Pixelgen chose open source (16:05)
              • Pixelator Python package (20:10)
              • Building within nf-core (21:40)
              • Florian - Biolizard (23:01)
              • Pipeline overview (25:19)
              • Using nf-core from a commercial setting (26:50)
              • Coming out of stealth (28:53)
              • Extending Pixelator (32:24)
              • Dealing with customers (34:58)
              • Looking to the future (39:38)
              • Interactive analysis (41:32)
              • Advice for others (43:12)
              • Pixelgen at the Nextflow Summit (45:16)
                • ...more
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