Episode 39: Spatial proteomics at Pixelgen

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)