🚀 Modules Team 🚀

27th-29th March 2023

The Hackathon March 2023 Project Board
The Group Discussion Channel #hackathon-march-2023-modules

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Modules Team


Team Leads

  • General advice, pointers, co-ordination etc.
    • Maxime Garcia (@maxulysse)
    • Matthias De Smet (@matthdsm)
    • Harshil Patel (@drpatelh)
    • Jonathan Manning (@pinin4fjords)
    • Nicolas Vannieuwkerke (@nvnieuwk)

  • Highly-multiplexed imaging subgroup
    • Adam Taylor (@adamjtaylor)
    • Florian Wuennemann (@FloWuenne)

But always ask first in: #hackathon-march-2023-modules!


Tasks Ideas

  • General development work
    • New modules
    • Fix modules tests
    • Improve modules

  • Highly-multiplexed imaging / Spatial Omics

Remember

  • Add yourself to Team Members slide
  • Assign yourself on issues on the project board
  • Post your progress here daily!
  • Sign up for a reviewing buddy (see slide)!

Team Members



Highly-multiplexed imaging subgroup


Reviewing Buddy List

Person A Person B
Bojan Darko
Kresimir Chiara
Aroj Margot
Jose Florian
Gordon Vojislav
Vojislav Gordon
Person A Person B
Fynn Paul
Marie Fynn
Paul Marie
Verena Alfred
Louisa Jasmin

Day One - Imaging I/IV

  • 🧡 #3090 - Background subtraction (KB)
    • [Monday, 3.30 CET] Assigned and in progress but no linked branch/PR CET
    • [EOD] figuring out passing optional inputs such as px size
    • [Tuesday AM] Working from nf-core but test dataset does not have the right metadata.
    • Small tonsil test data should work
    • Need to add columns to it
  • 🧡 #3089 - BaSicPy (VP)
    • [Monday, 3.30 CET] Assigned and in progress but no linked branch/PR CET
    • [EOD] looking at passing optional inputs. Issues with docker container working
    • [Tuesday AM]
  • 🧡 #3076 - Deepcell/Mesmer (CS, MI)
    • [Monday, 3.30 CET] Assigned and in progress but no linked branch/PR CET
    • [EOD] Passes testing with local data
    • Detail work for optional inputs ongoing
    • [Tuesday AM] Need image with membrane and nuclear marker
      (does this work? https://github.com/nf-core/test-datasets/pull/821)

Day One - Imaging II/IV

  • 🧡 #3065 - Coreograph (AH, MC)
    • [Monday, 3.30 CET] Assigned and in progress but no linked branch/PR CET
    • [EOD] Need to make bioconda package. Asking for help on this. (Really nice to have bioconda even if not strictly required)
    • To make seperate HackMD for technical details at this stage. Can skip bioconda tests manually
    • [Tuesday AM] Agree to skip bioconda for now with exceptions in test file,. Submit just DAPI from exemplar-001 as test-dataset
  • 🧡 #3044 - Mcquant (FW)
    • [Monday, 3.30 CET] Assigned and in progress but no linked branch/PR CET
      • Waiting on a suitable test-dataset from AT
    • [EOD] As above. Works on real data!
    • [Tuesday AM] Can test once test data is merged

Day One - Imaging III/IV

  • 💜 #2864 - Ilastik/pixelclassification (FW)
    • [Monday, 3.30 CET] Assigned and ready for review
      • PR #2875 approved by Nicolas Vannieuwkerke
        • 16.10 CET Merged!
    • [EOD] Conda tests skipped as has its own coda channel
  • 💜 #2865 - Ilastik/Multicut (FW)
    • [Monday, 3.30 CET] Assigned and ready for review
      • PR #2894 approved by Nicolas Vannieuwkerke, waiting for review by Maxime Garcia => Failing CI tests
    • [EOD] prettier lint failing. Request out on how to solve
    • 11.35 CET -> Merged

Day One - Imaging IV/IV

  • 🧡 #2477 - Mindagap/Mindagap (FW)
    • [Monday, 3.30 CET] Assigned and ready for review
      • PR #2477
      • Three reviewers assigned
      • Fails nf-core linting
    • [EOD] stub test needed
    • [Tuesday AM] Refactoring to add mandatory args
  • 🧡 #3095 - SpatialData/MCMICRO (WM, FW)
    • [Monday, 3.30 CET] Assigned and in progress but no linked branch/PR CET
    • [EOD] Docker image being built for this. Figuring out right output structure. Draft working
    • [Tues AM] Creating CLI tool. Looking for valid output directories.
  • 💚 #3100 - Scimap/MCMICRO (LKC, DM, CS)
    • [Monday, 16:00 CET] Worked on general structure
    • [EOD] First module attempt 🚀. Have basic structure but not working yet. Need to confirm right test data.
    • [Tues AM] Have positive results with test data. wiring parameters together. Used quantification test data.

Day One - New Modules I


Day One - New Modules II


Day One - New Modules I

Modules update


Day Two - New Modules


Day Two - Module updates


Day Two - Imaging Intro 1/6

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  • Multiplexed tissue imaging techniques such as CyCIF, CODEX and MIBI require several processing steps including registration, segmentation and quantification to provide cell-by-feature arays for dowstream analysis
  • MCMICRO is a nextflow pipeline for this, enabling scalable and robust analysis!
  • Teams at HMS, U Heidleberg and Sage Bionetworks are working add key tools as nf-core modules with a view to adding as a nf-core module (next hackathon goals!)
  • Join us in the #mcmicro channel or at mcmicro.org

Day Two - Imaging 2/6

🚀🎉 Merged!


Day Two - Imaging 3/6

  • 🧡 #3090 - Background subtraction (KB)
    • [Tuesday AM] Working from nf-core but test dataset does not have the right metadata.
    • Small tonsil test data should work
    • Need to add columns channels (to open PR)
  • 🧡 #3089 - BaSicPy (VP)
  • 🧡 #3076 - Deepcell/Mesmer (CS, MI)
    • [Tuesday AM] Need image with membrane and nuclear marker (can use tonsil test data (waiting on registered image))

Day Two - Imaging 4/6

  • 🧡 #3065 - Coreograph (AH, MC)
    • [Tuesday AM] Agree to skip bioconda for now with exceptions in test file,. Submit just DAPI from exemplar-001 as test-dataset
  • 🧡 #3044 - Mcquant (FW)
    • [Tuesday AM] Passing. Can test once test data is merged

Day Two - Imaging 5/6


Day Two - Imaging test data 6/6

Preparing end-to-end test datasets for imaging modules


Day Three Wrap Up: Modules


Day Three Imaging Summary

  • 🔬+🍏=❤️ Thank you for welcoming microscopists and image analysts into the nf-core community!
  • 🚀 11 modules started with several merged/lined up. We almost have a draft workflow for multiplexed image processing using all nf-core modules in place
  • 🤩 Huge shout out to Florian Wuennemann, Adam Taylor, Margot Chazotte, Jose Nimo, Chiara Schiller, Kresimir Bestak, Aroj Hada, Wouter-Michiel Vierdag, Luis Kuhn Cuellar, Carolin Schwitalla, Dominik Molitor, Jelena Pejovic Simeunovic, Svetozar Nesic and Emilio Palumbo
  • 🥳 Thank you for those who have reviewed and advised us!
  • 🔬 Join #microscopy on nf-core slack to bring more imaging to nf-core (MCMICRO+Janelia+EMBL-EBI+ more!)

Imaging Agenda for Weds AM

  • Todays goals
    • Remaining modules into PR and merge (expect slow down in tests)
    • Demo pipeline (from samplesheet, or revert to single file)

  • Blockers
    • BaSiCPy
      • Docker container not working for nextflow
      • Python script is parsing args in a odd way
      • Reqriting to use argparse.
      • This is for BaSicPy
  • Module status
  • Wrap up
    • Issues
    • Project board
    • HackMD
    • Planning Spreadsheet

  • Follow up on Slack
    • #microscopy (nf-core)
    • #mcmicro (HMS)
    • #mcmicro (nf-core)
  • Follow up on MCMICRO community call
    • Hackathon debrief
    • GalaxyME
  • Follow up on Bioconda environments
  • 🎉

Imaging Module Status


  • 💚 #3100 - Scimap/MCMICRO (LKC, DM, CS)
    • Streamlined some of the process, working but now testing with new test data
  • 🧡 #3065 - Coreograph (AH, MC)
    • Minor issue with versions being worked on
    • PR nearly ready
    • ~~AT to add test dataset once shared -sent on slack
  • 💚 #3090 - Background subtraction (KB)
    • Previous issues fixed. Adding test-datasets
    • Fixed versioning
    • passing Docker and Singularity tests with public dataset
    • PR ready for review


Merged!


Day Three - New Modules



Day Three - Module updates





🥳

Thank you to all who have worked on modules!


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