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BioImage.IO Meeting Minutes #28

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oeway opened this issue Jun 19, 2020 · 148 comments
Open

BioImage.IO Meeting Minutes #28

oeway opened this issue Jun 19, 2020 · 148 comments
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@cfusterbarcelo

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@oeway
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oeway commented Jun 19, 2020 •
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Hi,

The BioImage.IO team will meet every Wednesday 4PM CET, check the next meeting in your time zone.

Meeting Format

As discussed during in the AI4Life general assembly meeting (Oct. 10th, 2023), we will make the meeting more structured. For the first 15 minutes, we will take turns and having one presentation every week from one of the AI4Life partners, or guest speakers from community partners, developer etc.

The aim of the first 15-minute presentation is to provide community-friendly (especial for users and developers outside the AI4Life consortium) updates on new features, changes, announcements etc.

And the later part, we will have regular internal discussions or other relevant topics. Everyone is welcome to join the meeting via zoom: https://kth-se.zoom.us/j/65777152331, feel free to add your name and topic to the meeting agenda.
@oeway oeway mentioned this issue Jun 19, 2020
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oeway commented Jun 26, 2020 •
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June 26th, 2020

Attendees

Name affiliation username
Wei KTH @oeway
Esti UC3M @esgomezm
Hao KTH @haoxusci
Arrate UC3M @ArrateMunoz
Anna EMBL @akreshuk
Fynn EMBL @FynnBe
Maxim EMBL @m-novikov

Agenda + Minutes

  • All: general intro and your plans for the zoo in the near future

  • [name=Wei]:

    • updates on the new bioimage.io website
      • rebuild the website with a build system and CI
      • New UI design powered by Bulma
      • Support models, applications, notebooks, datasets
      • Support badges
      • Share the site template with other projects: covid19ai.io, shareloc.xyz etc.
      • Building backend (imjoy-ai-engine) for supporting uploading datasets and online inference service

  • [name=Anna] Technical question: single model with multiple weights, trained in different ways

  • [name=Anna] Other potential collaborators: ZeroCostDL4Mic

  • Discussion

    • How to support linking datasets with model weights and describe the training
    • Extend the model description spec, also for describing datasets, notebooks, applications

Note

  • How to group different cards
    • if only weights changed == same card
    • If postprocessing changed == different card

@constantinpape constantinpape mentioned this issue Jul 7, 2020
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oeway commented Jul 10, 2020 •
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July 10th, 2020

Attendees

Name affiliation username
Wei KTH @oeway
Esti UC3M @esgomezm
Daniel EPFL @dasv74
Anna EMBL @akreshuk
Carlos UC3M @carlosuc3m
Maksim Novikov EMBL @m-novikov
Ricardo Henriques IGC/UCL @paxcalpt

Agenda + Minutes

  • [name=Wei]

    • Updates for the website
      • resource description file
      • support links between items (apps to notebooks, dataset etc.)
      • support pagination
      • add ZeroCostDL4Mic and HPA as a community partner
      • comment feature powered by github
      • community partner
        • what's the criterion and procedure to join as a community partner?
          • Should we allow their own model zoo? (Think image.sc)
          • Open source? comercial partners?

            • Anna: accessible dataset, source of the model

            • Esti: published model without close dataset

            • Wei: sensitive medical data

            • Ricardo & Wei: Use badges to indicate and encourage

            • conclusion: give recommendation and show badges

          • Allow at least one admin of bioimage.io to access the repo?
            • conclusion: agreed
        • what kind of role and responsibility does the community partner have?
          • Contribute and maintain models/applications/notebooks
          • Accept third-party contribution if relevant? Say ilastik will in charge of all PRs for the ilastik models?
            • Anna: for long term, we should see more interoperatable models and that should go to BioImage.IO
            • for dedicated models that works for only one community partner, contribute to the partner instead of BioImage.IO

  • [name=Anna]

    • What examples do we need to add to make it easy for people to understand how to run models?

    • We should add a general "About" page describing what and why

      • Wei: Will do, this already been added for the community partners

  • [name=Daniel]

    • Demo of Model manager in DeepImageJ
    • Suggestions by Wei:
      • Add bug report button to link the same github issue as on BioImage.IO
      • Show linked items

  • [name=Esti]

    • Good practices uploading models; i.e. authorship & responsabilities
      • Anna & Ricardo: cite and acknowledge properly, typically it's fine to upload models that are derived from others' work
      • Wei & Ricardo: follow the license, most license will include terms about attribution

  • Discussion

    • What kind of users we are targeting with BioImage.IO

    • What's scope and focus of the bioimage.io platform? Should we only provide models, or including also the downstream/upstream utility tools for building workflow. The layout of the website.

    • How to upload a model compatible with different software? Same card / id besides proper reference?

      • Wei: use CI to automatically test the software compatibility, using BioEngine api
      • Anna: These tests should be done automatically

  • Suggestions

    • Daniel: Allow users to post images to the github issue for each model
    • Esti: support linking to image.sc
    • Ricardo: Network view for navigation

This was referenced Jul 10, 2020
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esgomezm commented Aug 6, 2020

July 24th, 2020

Attendees

Name affiliation username
Esti UC3M @esgomezm
Maksim Novikov EMBL @m-novikov
Arrate UC3M @amunoz
Constantin EMBL @constantinpape
Anna EMBL @akreshuk

Minutes

Discussion

  • What’s the distinction between models and notebooks
    -- DeepImageJ: Notebooks and Models are actually separate
    -- Notebook is used for training the model
    -- models are then only the train
    -- more general, how do we link models, notebooks (e.g. used to train the model) and datasets (e.g. where model was trained on)

  • datasets:
    -- how do we reflect “small” changes to the data-sets, e.g. fixing issues in the ground-truth
    -- public datasets can be “easily” added
    -- what about the private datasets?
    -- change the name? maybe "working data", "training data"

  • easier way to explore the models apart from search, ideas:
    -- “structured tag cloud”: selecting multiple tags to find a model that fits the “segmentation”, “electron-microscopy”, “membranes”, …

  • Discussion about the CZI Open Software call
    https://chanzuckerberg.com/rfa/essential-open-source-software-for-science/
    DeepImageJ is considering to apply; question is if/how to integrate the BioImage.io in there.
    Including Demo resources.
    Ilastik is also applying for the call, but for a different purpose?
    Are other community partners applying?
    If so, it would be nice if all could mention the model zoo.
    bioimage.io is not yet mature enough to apply on its own

  • once the website is more stable, we could start to write user facing docs
    a good example would be integration of the different community partners, e.g. train model in a ZeroCost notebook and run it with another community partner software

  • started discussion on interoperability between tools by community partners; big issue is (still :)) the different pre and post-processing steps that are implemented in a language specific manner. For now, porting between tools will probably be done manual by a developer of that tool.

  • When to change bioimage.io as landing page / reference model page for all community partners (e.g. for DeepImageJ, CSBDeep, ZeroCost home pages)? Then we could announce on image.sc etc. E.g. First of November. Discuss with Wei. Need to discuss with other community partners.

  • Citation discussion; how many citations to put in

Suggestions for the website

How do we make the website more intuitive for users?

Name-changes:

  • Change the name "Datasets" to "Training Data"; this should be clear for users.
  • Change the name "Models" to "Preconfigured Models"
  • Change the name "Notebooks" to "Code"

Could also go with more actionable names:

  • "Models" to "Find Models"
  • "Applications" to "Preview" or "Try on your data"?
  • "Notebook" to "Find Code"
  • "Datasets" to "Find Data"
  • Get rid of the "Application" button and just provide "Run" or "Demo" button on the model windows

Icons on the Model and Notebook Cards are different for the each Model / Network. This is confusing.

@oeway
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oeway commented Aug 21, 2020

BioImage.IO Meeting Minutes

August 21st, 2020

Attendees

Name affiliation username
Wei Ouyang KTH @oeway
Emma Lundberg KTH emmalundberg
Ricardo Henriques UCL / IGC @paxcalpt
Guillaume Jacquemet ÅAU/UTU @guijacquemet
Anna EMBL @akreshuk

Minutes

  • planning for the release of Bioimage.IO
    • release date: November 1st
    • features to offer by then:
      • display plain model cards for download
      • support interoperatability? @emma high priority
        • a list of useful/popular model, make sure it compatible with a few software. (show complementary with software rather than competition)
          • pytorch model (segmentation): ilastik, imjoy, zero
          • tensorflow model (denoising): zero, fiji, deepimagej, imjoy
          • classification: different types
          • starting from a training dataset? task?
      • use outline color encoding for types @anna
      • show text description for tags
      • online inference (single model, save it for the release)
      • model searching application (lower priority)
      • integration with colab, binder
      • community parties
        • guidelines for the community parter
        • short recommendation from all the community partner
        • feature models, sorting, popularity, model searching (lower priority)
      • Group the software by three types of tasks: 1) preprocessing/ annotation 2) training / transfer learning 3) prediction. Click a model, show a list of software grouped by tasks types
      • Improve 2h rendering interval @ricardo
      • parser script should validate the link, valide the fields, cover image size, add badges

@oeway oeway mentioned this issue Sep 4, 2020
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oeway commented Sep 4, 2020

September 4th, 2020

Attendees

Name affiliation username
Wei Ouyang KTH @oeway
Constantin Pape EMBL @constantinpape
Anna Kreshuk EMBL @akreshuk
Maksim Novikov EMBL @m-novikov
Fynn Beuttenmüller EMBL @FynnBe
Ricardo Henriques IGC/UCL @HenriquesLab
Estibaliz Gómez UC3M @esgomezm

Agenda

  • Wei
    • Outline color encoding
    • Zarr dataset and Vizarr
    • ImageJ.JS
    • discussion
      • Run DeepImageJ models
      • Model conversion service
        • BioEngine Application running on Binder
        • Tensorflow to Tensorflow.JS
        • PyTorch to ONNX to Tensorflow?
      • RPC link between the website and software
        • From the website: Send model from the website to Ilastik/Fiji etc.
        • From the software: launch model browser
        • Example PycroManager
  • Ilastik
    • Specification of training, Application specific?
    • Website header too large?

Minutes

  • Add underline color LUT
  • What models to use as show case
    • 2D Unet / Nuclei Broad
    • 3D Unet
  • Token (url) for linking model across software
  • Roadmap general issue
  • Training:
    • descriptive training procedure is too ambitious
    • instead: partners can support their own training procedures; training APIs can be shared
    • example: ilastik will have a training API that can also be exposed through imjoy RPC so it could be used from the browser

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oeway commented Sep 18, 2020

September 18th, 2020

Attendees

Name affiliation username
Wei Ouyang KTH @oeway
Anna Kreshuk EMBL @akreshuk
Carlos García UC3M @carlosuc3m
Estibaliz Gómez UC3M @esgomezm
Novikov Maksim EMBL @m-novikov
Florian Jug CSBD + HT @fjug
Fynn Beuttenmüller EMBL @FynnBe
Maksim Novikov EMBL @m-novikov

Agenda

  • Roadmap general issue
    • Model runners
    • Improve Landing
    • Documentation
    • animal icon?
    • Run button for each model
    • (Simple) models which can be run in multiple applications. E.g. train a model in a notebook in ZeroCost, run in both DeepImageJ and CSBDeep (or ilastik) (note: deal with output error produced by different framework)
  • Cross-compatibility of models - how much can we guarantee for a model following the specs?
  • Generic model runner (two runners, PyTorch and Tensorflow) to have the same as HPA model runner for all models?
  • What should really be in the "Applications" part?
  • New applications: CellPose, ImageJ.JS, CellPose-ImageJ.

@oeway oeway mentioned this issue Sep 20, 2020
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oeway commented Oct 2, 2020 •
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October 2nd, 2020

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Florian Jug CSBD + HT @fjug
Dominik Kutra EMBL @k-dominik
Jan Funke Janelia @funkey
Carlos García UC3M @carlosuc3m
Estibaliz Gómez UC3M @esgomezm
Arrate Muñoz UC3M @arratemunoz

Agenda

  • Florian

    • Pitch the model zoo project

  • Wei

    • Updates on the bioimage.io website

    • BioEngine API for model runners

      api.registerService({
   "type": "model-runner",
   "init": init, // initialize the runner
   "predict": predict, // perform prediction
   "fit": fit // perform training (optional)
})

      Alternatively, we can use scikit-learn style with fit and transform function.

      • ilastik
      • deepimagej
        • support via pyimagej
        • support via imagej.js

    • Demo for a new model: Learn2Sofie

  • Jan

    • Introduction about the live supervised learning platform at Janelia

  • Anna and Wei

    • plan for the November release, implementation of the model runners.

@oeway
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oeway commented Nov 5, 2020

October 30th, 2020

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Anna Kreshuk EMBL @akreshuk
Tom Burke CSBD @tomburke-rse
Florian Jug CSBD + HT @fjug
Deborah Schmidt CSBD @frauzufall
Arrate Muñoz UC3M @arratemunoz
Anna Kreshuk EMBL @akreshuk
Novikov Maksim EMBL @m-novikov
Fynn Beuttenmüller EMBL @FynnBe
Dominik Kutra EMBL @k-dominik
Estibaliz Gómez UC3M @esgomezm

Agenda

  • Discuss the test_inputs and test_outputs format: will be feeded as a list and use npy as the only formats, this will be specifically used for CI testing, but combined with converters, for the users, we can use another field, e.g. test_samples
  • Change normalization to preprocessing, and agreed on several types of preprocessing functions
  • The model file can contain multiple formats of the same weights, the weights is a dictionary which uses a unique format string as the key

See also in the project: https://github.com/orgs/bioimage-io/projects/1

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oeway commented Nov 16, 2020

November 13th, 2020

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Anna Kreshuk EMBL @akreshuk
Tom Burke CSBD @tomburke-rse
Florian Jug CSBD + HT @fjug
Deborah Schmidt CSBD @frauzufall
Arrate Muñoz UC3M @arratemunoz
Anna Kreshuk EMBL @akreshuk
Novikov Maksim EMBL @m-novikov
Fynn Beuttenmüller EMBL @FynnBe
Dominik Kutra EMBL @k-dominik
Estibaliz Gómez UC3M @esgomezm
Constantin Pape EMBL @constantinpape
Carlos García UC3M @carlosuc3m

Agenda

  • 0.3.0 project: https://github.com/orgs/bioimage-io/projects/1

  • Authors in weights vs. authors in model

    • 3 parties to give credit to:
      • Who is the creator of the bioimage.io.model.zip?
        The creator in the yaml points that out. The top-level description describes the training setup, purpose, etc.
      • Who is the creator of the type of model?
        The existing list of citations is good enough!
      • Who trained the linked weights?
        If not the same as the creator of the model, names can be given here. Description field is superfluous and needs to be removed here!

  • Weights-formats we support:

    • tensorflow_saved_model_bundle: Zip the weights and the folder with the variables and link to this zip from the yaml-file. (File name: *.zip)
    • keras_hdf5:
    • tensorflow_js: a json file + binary weights files
    • pytorch_state_dict:
    • pytorch_script:

  • Naming convention for the model bundle: *.bioimage.io.model.zip

  • show a table with features (weights format, pre/post processing types) that are implemented by consumers

@FynnBe FynnBe mentioned this issue Nov 20, 2020
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oeway commented Nov 20, 2020

November 20th, 2020

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Anna Kreshuk EMBL @akreshuk
Florian Jug CSBD + HT @fjug
Deborah Schmidt CSBD @frauzufall
Arrate Muñoz UC3M @arratemunoz
Anna Kreshuk EMBL @akreshuk
Novikov Maksim EMBL @m-novikov
Fynn Beuttenmüller EMBL @FynnBe
Dominik Kutra EMBL @k-dominik
Estibaliz Gómez UC3M @esgomezm
Constantin Pape EMBL @constantinpape
Carlos García UC3M @carlosuc3m
Ricardo Henriques IGC & UCL @HenriquesLab

Project: https://github.com/orgs/bioimage-io/projects/1

Agenda

  • Suggested Agenda Points from Dresden
    • I2K - 0.3.0 releases? Our own dialects? What are our goals?
      • Let's make it 0.3.0 and not any of our dialects!
    • More generally: when and how would 0.3.0 count as 'released'? How can we ensure that the released state leaves no margin for interpretation? (Example: how would I find out what parts are optional?)
      • For now, the readme in the repo is the full spec. We will soon release on GitHub the 0.3.0 version and that's it!
    • (Minor?) Pre/-Postprocessing: could axis-concept be more ubiquitously supported? (Example: Pre::zero_mean_unit_variance vs. Post::scale_linear)
      • We will add axis to scale_linear (and maybe more?) after I2K and freeze 0.3.0 in its current form.
    • Input/Output types or class? Example: if you have a model that gets/produces an image and a table of datapoints. How would I know what is what? Where would I specify this best? (Wei: Hints for rendering of inputs/outputs tensors for UI, proposal)
      • Let's start a 0.3.1 branch and get going. Plenum discussion after I2K in December...
  • How do we distinguish between the models that do not need pre/post-processing and the ones that cannot be described with the defined steps?
    • DD thinks: In that case we use the 'source'-tag... (and we do that already for N2V).
  • Metadata of the images and numpy arrays?

Decided:

  • blow up if config key contains anything unfamiliar
  • custom pre / postprocessing should also go into the config

TODO befor releasing 0.3.0:

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oeway commented Dec 4, 2020

November 27th, 2020

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Anna Kreshuk EMBL @akreshuk
Deborah Schmidt CSBD @frauzufall
Tom Burke CSBD @tomburke-rse
Arrate Muñoz UC3M @arratemunoz
Fynn Beuttenmüller EMBL @FynnBe
Estibaliz Gómez UC3M @esgomezm
Constantin Pape EMBL @constantinpape
Novikov Maksim EMBL @m-novikov
Carlos García UC3M @carlosuc3m
Daniel Sage EPFL @dasv74

Project: https://github.com/orgs/bioimage-io/projects/1

Agenda

  • What's left to do before releasing 0.3.0?

Outcome

More user-friendly website

  • add a introductory tour with several steps (easy option would be a tutorial video)

Dev documentation

  • improve md based spec documentation

Run torchscript (e.g. models from deepImageJ) in ilastik, (after ilastik can parse 0.3.0)

Autogenerating the spec documents from yamls or spec parser

@oeway
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oeway commented Dec 11, 2020

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Anna Kreshuk EMBL @akreshuk
Tom Burke CSBD @tomburke-rse
Arrate Muñoz UC3M @arratemunoz
Fynn Beuttenmüller EMBL @FynnBe
Estibaliz Gómez UC3M @esgomezm
Constantin Pape EMBL @constantinpape
Novikov Maksim EMBL @m-novikov
Daniel Sage EPFL @dasv74
Florian Jug CSBD + HT @fjug

Agenda

@oeway
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oeway commented Dec 18, 2020

December 18th, 2020

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Anna Kreshuk EMBL @akreshuk
Fynn Beuttenmüller EMBL @FynnBe
Constantin Pape EMBL @constantinpape
Florian Jug CSBD + HT @fjug
Carlos García UC3M @carlosuc3m

Project: https://github.com/orgs/bioimage-io/projects/1

Agenda

We have a very short meeting today, but still quite fruitful for finalising the last pieces left for v0.3.0!

Update to configuration: bioimage-io/spec-bioimage-io#59
Update to update: bioimage-io/spec-bioimage-io#61

Data type and data range: bioimage-io/spec-bioimage-io#55 (comment)

@oeway oeway mentioned this issue Dec 18, 2020
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@m-novikov m-novikov pinned this issue Jan 15, 2021
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oeway commented Jan 15, 2021

January 15th, 2021

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Daniel Sage EPFL @dasv74
Tom Burke CSBD + MPI-CBG @tomburke-rse
Constantin Pape EMBL @constantinpape
Ricardo Henriques IGC & UCL @HenriquesLab
Estibaliz Gómez UC3M @esgomezm
Arrate Muñoz-Barrutia UC3M @arratemunoz
Jan Philipp Albrecht MDC @jpalbrecht
Deborah Schmidt MDC @frauzufall
Carlos García UC3M @carlosuc3m
Anna Kreshuk EMBL @akreshuk
Fynn Beuttenmüller EMBL @FynnBe
Maksim Novikov EMBL @m-novikov

Agenda

  • News: BioImage Model Zoo featured on Nature news https://www.nature.com/articles/d41586-021-00023-0

  • Documentation

    • User Guide
      • Overview
        • Add the cross-compatibility table
      • Tutorials
        • including videos
      • How-tos Guides
        • How to choose a model for my data
        • How to run this model in community partners' tools
        • How to search by tags
      • Explanations
        • The risk of model mismatch
    • Model Developers
      • Tutorial
      • How-tos Guides
        • How to make a model package
    • Application Developer
      • Tutorial
      • How-tos Guides
        • How to become a community partner
        • How to build a BioEngine App
      • Explainations
        • Responsibilites for community partners
      • API reference

  • Vision

    • Advanced AI models in one-click

  • Roadmap

    • Runners support 0.3.0; tests for runners and models; CI
    • Each model should be associated with at least one model runners
    • Support type info for guide the rendering of inputs/outputs tensors
    • A new tab for hosting scripts? (e.g. Fiji/ImageJ macro, similar to notebooks)
    • RPC interface
      • Support making RPC calls to local software
      • Connect model API servers for support cloud based training and inference (e.g.: cellpose)

  • Timeline / meetings

    • 3 weeks from now (Feb. 5th): compatibility hackathon
      • Ilastik, DeepImageJ, ImJoy, Zero?, Fiji
    • 5 weeks from now (Feb. 23rd): documentation polish
    • end of February: guinea pig users and contributors experiment
    • early March: release!

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oeway commented Jan 22, 2021

January 22nd, 2021

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Tom Burke CSBD + MPI-CBG @tomburke-rse
Constantin Pape EMBL @constantinpape
Estibaliz Gómez UC3M @esgomezm
Arrate Muñoz-Barrutia UC3M @arratemunoz
Jan Philipp Albrecht MDC @jpalbrecht
Fynn Beuttenmüller EMBL @FynnBe
Maksim Novikov EMBL @m-novikov

upcoming Hackathon project: https://github.com/orgs/bioimage-io/projects/2

Agenda

  • TODOs before the hackathon

  • Hackathon planning
    Main goal: convert to different formats (e.g.: ONNX)

    • Currently supported model formats:

      • tiktorch (pytorch, torch script, onnx)
      • deepimagej (torch script, tensorflow saved model, keras h5)
      • Fiji (tensorflow saved model)
      • ImJoy (support all types of models with different plugins, including onnx, onnx.js, tensorflow.js)

    • Model cross-compatibility aims:

      • tiktorch <-> deepimagej (torch script)
      • tiktorch -> ImJoy (onnx)
      • ImJoy -> deepimagej (tensorflow saved model)
        Idea: all the consumer convert their model into onnx, and use it as a neutral model representation, which can be further converted into other formats.

    Date: Feb. 5th, 9am - 6pm

left for future agenda

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oeway commented Jan 29, 2021

January 29th, 2021

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Tom Burke CSBD + MPI-CBG @tomburke-rse
Constantin Pape EMBL @constantinpape
Estibaliz Gómez UC3M @esgomezm
Arrate Muñoz-Barrutia UC3M @arratemunoz
Jan Philipp Albrecht MDC @jpalbrecht
Fynn Beuttenmüller EMBL @FynnBe
Maksim Novikov EMBL @m-novikov
Constantin Pape EMBL @constantinpape
Carlos García UC3M @carlosuc3m

Project: https://github.com/orgs/bioimage-io/projects/1

upcoming Hackathon: https://github.com/orgs/bioimage-io/projects/2

Agenda

  • Generate CI error report for Models

The idea is to provide a link to the CI status as an additional field in the manifest.bioimage.io.yaml file: {"ci_status": "url"}

Then the link point to a json file contains CI status for the models:

{
    "name": "Ilastik CI",
    "timestamp": "2021-xsssxxx",
    "status": "",
    "error": "",
    "models": {
        "<Model ID>": {"status": "pass", "error": ""},
        
    }
}

The <Model ID> is the same as here: https://github.com/deepimagej/models/blob/master/manifest.bioimage.io.yaml#L38

This json file can be uploaded to a separate branch of the model repo, and this is an example which contains Github Actions configurations for uploading artefacts to another branch: https://github.com/bioimage-io/bioimage-io-models/blob/master/.github/workflows/compile-manifest.yml

The CI status json file will be loaded from the website and rendered as badges for model status.

@oeway
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oeway commented Feb 5, 2021

BioImage.IO Hackathon on Model Cross-compatibility

Feburary 5th, 2021

Attendees

Name affiliation username (github)
Tom Burke CSBD + MPI-CBG @tomburke-rse
Wei Ouyang KTH @oeway
Estibaliz Gómez UC3M @esgomezm
Constantin Pape EMBL @constantinpape
Joran Deschamps MPI-CBG @jdeschamps
Maksim Novikov EMBL @m-novikov
Romain F Laine MRC-LMCB, UCL @Romain-Laine
Guillaume Jacquemet ÅAU @guijacquemet
Carlos García UC3M @carlosuc3m
Florian Jug (dropped by) CSBD + MPI-CBG @fjug

Project: https://github.com/orgs/bioimage-io/projects/1

upcoming Hackathon: https://github.com/orgs/bioimage-io/projects/2

Agenda

  1. Brainstorming on what model/approach to work with
    Please write the potential model/apporach you can potentially work on here:
  • Pytorch - TorchScript compatibility
  • ONNX weight format
  • bundling TensorFlow models directly from python (under development https://github.com/deepimagej/pydeepimagej/tree/bioimage-yaml)
  • linking material from other community partners in manifest.yaml (e.g. ZeroCostDL4Mic notebooks with bundled models)
  • update CSBDeep python and java parts to 0.3.0 + model runner integration into fiji
  • List the versions we are compatible with. e.g. Fiji supports TF until 1.15
  • Import ONNX models to ZeroCostDL4Mic for transfer learning and export models using ONXX for using models in other tools.
  • numpy reader for ImageJ/Fiji(?)

@wei - ImJoy

  • Loading DeepImageJ/FIji models via PyImageJ

  • ONNX.js models

  • Tensorflow.js models

  • tried ONNX.js multiple version: didn't work with the Unet model

@constantinpape - Ilastik

  • onnx models
  • torchscript models

@esti - DeepImageJ

  • tensorflow saved_model.pb
  • Pytorch - torchscript

@tom - Fiji/CSBDeep

  • Tensorflow1 saved models

@joran

  • ONNX version of imagej-tensorflow

@m-novikov

  • running tensorflow models (e.g. U-Net pancreatic cell segmentation)
  1. Work on the models
  1. Debriefing

  • Demo for running ONNX runtime

    • TODO: make docs for loading yaml and do inference using ONNX runtime

  • Changes in the spec 0.3.1 to support multiple version of the same weight format
    Proposal:

    • onnx:
      - sha256: 5bf14c4e65e8601a
      source: ./weights_opset11.onnx
      opset_version: 11
      parent:
      - sha256: 5bf14c4e65e86
      source: ./weights_opset12.onnx
      opset_version: 12
      test_outputs: ["test_output_onnx_opset_12.npy"]
      parent:
    • Dimension ordering for different formats? (e.g. Pytorch vs Tensorflow)
      Proposal: Add transpose_axis for different dimension ordering

  • ONNX version

Framework ONNX opset_version comment
ONNX runtime (Python)
ONNX runtime (Java) 12 version: 1.6.0
ONNX.js 9
onnx2keras
keras2onnx
  • Support Unet in different consumers
Consumers Works? comment
pytorch -> onnx(ilastik) yes except the output border
pytorch -> torchscript(deepimagej) yes except the output border (it works without tiling)
pytorch -> onnx(ONNX.js) No blocked
onnx -> keras (zero) No blocked
keras -> onnx (zero) ?
Fiji ?

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oeway commented Feb 12, 2021

Feburary 12th, 2021

Attendees

Name affiliation username (github)
Tom Burke CSBD + MPI-CBG @tomburke-rse
Wei Ouyang KTH @oeway
Estibaliz Gómez UC3M @esgomezm
Constantin Pape EMBL @constantinpape
Joran Deschamps MPI-CBG @jdeschamps
Maksim Novikov EMBL @m-novikov

Project: https://github.com/orgs/bioimage-io/projects/1

Hackathon: https://github.com/orgs/bioimage-io/projects/2

Agenda

@oeway
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oeway commented Feb 19, 2021 •
edited

Feburary 19th, 2021

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Estibaliz Gómez UC3M @esgomezm
Anna Kreshuk EMBL @akreshuk
Maksim Novikov EMBL @m-novikov
Jan Philipp Albrecht MDC @jpalbrecht

Project: https://github.com/orgs/bioimage-io/projects/1

Hackathon: https://github.com/orgs/bioimage-io/projects/2

Agenda

  • Plan for the upcoming hackathon on documentation

    • Discuss the priority for the release
    • How to contribute models
    • Model Documentation Templates with Runner
    • Focus more on the developers

  • Website updates:

    • Running pybio spec verification in the root model repo and add error information if a model fails
    • Displaying a spec badge with passing and failing status for all the models, please fix all the failing models!
    • Resource Item ID rule change: they will be all prefixed with the collection/partner ID, e.g.: deepimagej/WidefieldFitcSuperResolution

  • Upcoming changes:

    • Add a new tab about scripts
    • Improve the BioEngine, Model runner interface change
      • Support Ilastik/Tiktorch model runner
      • Support DeepImageJ.JS

@oeway
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oeway commented Feb 23, 2021

BioImage.IO Hackathon on Documentation

Feburary 23rd, 2021

Attendees

Name affiliation username (github)
Tom Burke CSBD + MPI-CBG @tomburke-rse
Wei Ouyang KTH @oeway
Estibaliz Gómez UC3M @esgomezm
Arrate Muñoz-Barrutia UC3M @arratemunoz
Anna Kreshuk EMBL @akreshuk
Fynn Beuttenmüller EMBL @FynnBe

Project: https://github.com/orgs/bioimage-io/projects/1

Hackathon: https://github.com/orgs/bioimage-io/projects/2

Agenda

  • Hackathon Documentation (https://bioimage.io/docs/)
    • Discuss the priority for the release
    • How to contribute models
    • Model Documentation Templates with Runner
    • Focus more on the developers
    • Roadmap

Proposals

1.- What is the bioimage model zoo? It is more than advance AI models in one click, no?

  • "About" button. It points to https://github.com/bioimage-io/bioimage-io-models.
  • I would add a simple graphical schema about how to contribute, inputs and outputs of the bioimage.io to get a general idea about all the environment (google drawings?)
  • In the contribution text, it says: "You are welcome to submit your models, datasest, applicattionionss and Jupyter notebooks to BioImage.IO." Maybe the main first description should be also oriented into this.

2.- Contributions: Can you contribute in any other way besides being a developer?

  • User: feedback as a user. Through communication channels. GitHub chat. You need to sign

  • Contribute the models to the website (main)

    • Contribute weights to existing models.

  • Contribut to the development of the zoo through GitHub.

  • Contribute to the runners.

  • Consumer software.

  • Bioengine apps.

3.- Model contribution requirements

  • The models that are upload should run at least in one community partners

  • In the begining we need to support people's contributions.

  • How does the developer decide the consumer software? Decision tree with some easy features (TF or PyTorch for example)

  • The model HAS TO BE in the 0.3.0 format.

  • Central repo where the developer can do a PR. There is a Bioimage Model repo.

  • How to contact:

    • image.sc (join the community partner? tag: bioimagemodelzoo?)
    • github issue
    • gitter

  • What are the requirements in terms of compatibility with community partners to contribute a dataset, a notebook, a model, or a workflow?

    • goto the central repo

  • What if a model cannot be loaded in any of the software? and if I provide the notebook? e.g. from https://github.com/bioimage-io/bioimage.io/blob/master/docs/resource-description-file.md#describing-ai-models, it could be assumed that almost anything can be loaded

    • This would be a special contribution. You will always need to provide a model example with the 0.3.0 format.
    • Models have attachments? The notebook could be in the attachment.

  • If I want to contribute with a model, should I create the spec and then ask a partner to include the model in its github with a PR? --> Central repo

  • Could we provide the link to the repo of each community partner to make the RDF and manifests more accessible?

  • This info is now at https://github.com/bioimage-io/bioimage.io/blob/master/docs/contribute.md

  • Description of the RDF and the manifest. Sometimes they seem to be the same and other times, not.

3.- Resource Description File.

  • The main and basic file to write is the RDF --> link to the description and examples/templates (these can be some datasets or notebooks already available). 
  • Sometimes in the text, it is used "model zoo specification" and others, Resource Description File.
  • RDF version is 0.2.0. Most probably the entire document should be reviewed: https://github.com/bioimage-io/bioimage.io/blob/master/docs/resource-description-file.md
  • The name of the RDF should be manifest.bioimage.io.yaml?
  • What is the main structure of this document and how do I start including my notebooks, datasets, and models?
  • Section "Describing AI models": how do you feel about merging it with the configuration specification? or make it very clear that there are two kinds of descriptions: for interoperable models and for just models. 

4.- Configuration specifications:

  • The example is missing, the link is broken.
  • Preprocessing and post-processing reference implementations or mathematical methods. 
  • Run modes specification is still empty. If it is free, then the spec checker should avoid this field. Also, if it is free, shouldn't it go in the config?

5.-Join as a community partner

6.- Doc for bioengine-apps

7.- Template https://deploy-preview-89--bioimage.netlify.app/docs/#/

8.- Tutorials

  • Videos
  • Embed the model runner in the page

Outcomes:

@oeway
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oeway commented Mar 5, 2021

March 5th, 2021

Attendees

Name affiliation username (github)
Tom Burke CSBD + MPI-CBG @tomburke-rse
Wei Ouyang KTH @oeway
Estibaliz Gómez UC3M @esgomezm
Arrate Muñoz-Barrutia UC3M @arratemunoz
Maksim Novikov EMBL @m-novikov
Anna Kreshuk EMBL @akreshuk
Fynn Beuttenmüller EMBL @FynnBe
Daniel Sage EPFL @dasv74
Jan Philipp Albrecht MDC @jpalbrecht
Florian Jug CSBD + HT @fjug

Agenda

  • Solving the failing tests

    • make git_repo optional
    • make cite as optional

  • Zenodo integration to simplify model upload

    • Automatic yaml config generation
    • Model upload
    • tags: bioimage-io for model discovery

  • Standardisation of the title of the pre-trained mode: some of them include U-Net, or not, some of them highlight the application "Cell segmentation". The front page seems a little weird because the name of models are not unified.

    • [TODO] Add recommendation about titles (mind set: what it does NOT what it is (e.g. U-Net))
    • [TODO] Update our core model titles
    • [TODO] Add recommendation for the covers with image before and after; If it is not image-to-image, the developer should find a way to illustrate whan the model does.

  • Smaller issues around the website:

    • Need a contact button and some e-mail to reach out to stakeholders. Can we have an e-mail at the bioimage.io domain?

      • Add an contact email to the about tab
      • Add issue page to the about tab

    • About button should be updated to contain About from docs

      • Update text in the About dialog

    • Contribute button is right now showing an old github post instead of actual guidelines

      • redirect user to the contributon in the docs

    • The bolding of the model or application word is too subtle

      • update the color

@oeway
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oeway commented Nov 8, 2023

November 8th 2023

Attendees

Name affiliation username (github)
Iván Hidalgo IGC @IvanHCenalmor
Wei Ouyang KTH @oeway
Jeremy Metz KTH @jmetz
Weize Xu KTH (visiting) @Nanguage
Estibaliz Gómez IGC @esgomezm
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Mariana Ferreira IGC @mariana-gferreira
Arrate Muñoz UC3M @arratemunoz
Anna Kreshuk EMBL @akreshuk

Agenda

  • BioImage.IO community google groups
  • Synergy between docker container efforts, instead of creating separate docker containers for each notebook, try to wrap it as a conda-pack file for the environment and provide a model.py file, then it can reuse the models in the BioEngine. Example for a model: https://github.com/bioimage-io/bioengine-model-runner/tree/main/src/bioengine-model-runner And here is the public model repostiroy, with models and also the shared conda environements: https://uk1s3.embassy.ebi.ac.uk/model-repository
    • Packages which doesn work inside container on mac host system: imagecodecs
  • BioEngine Desktop
    • Using podman desktop
    • Add BioEngine container features
  • Updates about the core library
  • Demo for the new test run
  • paper status
    • CI for figure out what can run what
    • Fix the test run
    • Upload
  • rdf.yaml naming discussion
    • Not changing now, postpone the dicision

@cfusterbarcelo
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November 15th 2023

Attendees

Name affiliation username (github)
Iván Hidalgo IGC @IvanHCenalmor
Estibaliz Gómez IGC @esgomezm
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Mariana Ferreira IGC @mariana-gferreira
Joran Deschamps HT @jdeschamps
Luis Kuhn Cuellar QBiC-Tübingen @luiskuhn
Mehdi Seifi HT @mese79
Vera Galinova HT @veegalinova
Fynn Beuttemueller EMBL Heidelberg @FynnBe

Agenda

  • Presentation from QBiC Tuebingen (Luis Kuhn Cuellar): Quantitative Biology Center
    • Their goal is to contribute and consume models to the BMZ
    • mlf-core docs
  • (Joran) Deep learning specs and recommendations for OME-NGFF
    • Working group to draft use cases
    • Assert compatibility of current OME-NGFF specs
    • Open issue on OME-NGFF
    • Put out recommendations for DL-specific Zarr data organization
  • What to do with a model that we know that is wrong?
    • Delete it?

@cfusterbarcelo
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November 22th 2023

Attendees

Name affiliation username (github)
Iván Hidalgo IGC @IvanHCenalmor
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Mariana Ferreira IGC @mariana-gferreira
Joran Deschamps HT @jdeschamps
Mehdi Seifi HT @mese79
Vera Galinova HT @veegalinova
Jeremy Metz KTH / Scilifelab @jmetz
Daniel Franco DIPC / EHU @danifranco
Weize Xu KTH (visting) @Nanguage

Agenda

@oeway
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oeway commented Dec 6, 2023

November 6th, 2023

Attendees

Name affiliation username (github)
Iván Hidalgo IGC @IvanHCenalmor
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Mariana Ferreira IGC @mariana-gferreira
Joran Deschamps HT @jdeschamps
Mehdi Seifi HT @mese79
Vera Galinova HT @veegalinova
Jeremy Metz KTH / Scilifelab @jmetz
Daniel Franco DIPC / EHU @danifranco
Weize Xu KTH (visting) @Nanguage
Florian Jug HT @fjug
Arrate Muñoz UC3M @arratemunoz

Agenda

@oeway
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oeway commented Dec 7, 2023

December 6th 2023

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Iván Hidalgo IGC @IvanHCenalmor
Anna Kreshuk EMBL @akreshuk
Mariana Ferreira IGC @mariana-gferreira
Joran Deschamps HT @jdeschamps
Mehdi Seifi HT @mese79
Vera Galinova HT @veegalinova
Jeremy Metz KTH / Scilifelab @jmetz
Daniel Franco DIPC / EHU @danifranco
Weize Xu KTH (visting) @Nanguage
Florian Jug HT @fjug
Estibaliz Gómez IGC @esgomezm
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano

Agenda

  • CI for the uploading discussion (Fynn & Jeremy)
  • Piximi (Nodar) might interested in working with us on the docker solution for the bioengine
  • Enable CI for deepimagej (it was disabled to not )
  • New community partner: BiaPy
  • Dog Food Hackathon at EMBL (11th-15th March, 2024)
  • Updates on new test run feature using imagej.js
    • Using imagej.js to load images with more file format support
    • Support "arbitrary" image shape through padding and tiling
  • Format for the next meetings - Proposal
    • Open rolling notes, GDrive
    • Linked from the GitHub issue
    • Establish a system to rotate through partners
    • Structure: 10-15 mins presentation, rest is discussion around proposed topics
    • When do we implement it? January 2024

@cfusterbarcelo
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December 13th 2023

Attendees

Name affiliation username (github)
Iván Hidalgo IGC @IvanHCenalmor
Mariana Ferreira IGC @mariana-gferreira
Estibaliz Gómez IGC @esgomezm
Carlos García Pasteur @carlosuc3m
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano

Agenda

  • Advanced postprocessing:

    • Curtis wanted to develop a cross operator so python and java become compatible and then, we would not neet to reimplement post and preprocessings in java as well.

  • Abhishek Bhardwaj joined the meeting representing empanada model (Panoptic DeepLab + some important bells and whistles)

    • They have an entire pytorch_state_dict with the complex postprocessing already included. They have also a ready to upload zip file that will be shared by email to check it. In the long term, they'll try working on torchscript for full cross-compatibility

  • (Esti, not super important still claimed by users) Access to data programmatically: if this is in the roadmap as a future development, it would be interesting to add a download api in the model card as well. (PD: at the moment, the link in the download buttom of all the datasets points to the official distribution site and is good in all cases.)

    • More for the future (to discuss with Fynn and add this lines in the roadmap)

  • (Esti) Pre/post-processing: how easy or difficult is it to contribute to it without being the main developer? Is it modular? A fast/quick mechanism to add those (also in the specs), may be interesting for:

    • (without assuming that the list of pre/post-processing is going to be static) Easily integrationin both python and java, preserving some synchronisation and easy testing.
    • Supporting new commers to keep updating the library in an easier way.
    • New community partners who already have their "definition" and requirements of pre/post-processing. The easy integration of such requirements would facilitate specs adoption and integration of the bioimageio.core library. This would also speed up the cross-compatibility.
    • It's true that they should be basic processings to keep everything simple but some make sense to integrate (like downsampling images or extremely popular models such as cellprofiler and stardist).

  • Fynn presenting a roadmap for pre and post-processing status in January/february

    • Tomaz: if the spec is well structured and documented, it should not be an issue to reimplement these steps.
    • Esti: somehow for sustainability, someone should be developing it or making this real.

  • (Esti) When opening an issue in the model card, the author/maintainer of the model does not receive any email, so it's hardly difficult to automatically aware it about any potential problem with the model. Example here: StarDist Plant Nuclei 3D ResNet collection-bioimage-io#652 (comment)

    • Our own log in system for the model upload and bioengine, and also for the interaction with the user/maintainer.
    • Jeremy: there is already a log in working. This one is for uploading models and in the future, use the server, gpus or any other computational resources.
    • In this system, the conversations and issues about each model will be stored as json file. Then a search system could be developed.

@jmetz
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jmetz commented Jan 10, 2024

December 20th 2023

Attendees

Name affiliation username (github)
Iván Hidalgo IGC @IvanHCenalmor
Mariana Ferreira IGC @mariana-gferreira
Estibaliz Gómez IGC @esgomezm
Carlos García Pasteur @carlosuc3m
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano

Agenda

  • The upload is still down. When a model is uploaded through zenodo, it is not published in the BioImage Model Zoo.
  • New meeting structure: keep HackMD format. Add only rotation among partners

Next meeting agenda

@oeway
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oeway commented Jan 17, 2024

January 17th 2024

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Jeremy Metz KTH / Scilifelab @jmetz
Anna Kreshuk EMBL @akreshuk
Joran Deschamps HT @jdeschamps
Mehdi Seifi HT @mese79
Vera Galinova HT @veegalinova
Iván Hidalgo IGC @IvanHCenalmor
Estibaliz Gómez IGC @esgomezm
Arrate Muñoz UC3M @arratemunoz
Matthew Hartley EBI @matthewh-ebi

Agenda

  • New meeting format
  • WP6 update: Presentation (slides)
    • Anna suggested getting in touch with Globias for the reviewing
    • Matthew also suggested the Tuesday interest group meeting (organized by Aastha)
    • Discussed MP from partners on tasks 6.1 and 6.2 (grant agreement)
    • CellPose in browser would be incredibly useful for the OC (could be potentially logged as MP)
    • RandomForest tasks (consultation or OC projects) could be kicked towards EMBL-HD
    • Involve Wei and Anna in the OC discussions and selection of the OC team for this year
  • Status of the new upload feature
  • BioEngine triton launcher, support deploying custom cellpose models and training
  • Test Run on large images: Neuron Segmentation in EM (Membrane Prediction) collection-bioimage-io#484 (comment)

@esgomezm
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January 24th 2024

Attendees

Name affiliation username (github)
Jeremy Metz KTH / Scilifelab @jmetz
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Joran Deschamps HT @jdeschamps
Mehdi Seifi HT @mese79
Iván Hidalgo IGC @IvanHCenalmor
Estibaliz Gómez IGC @esgomezm

Agenda

  • Presentation AI4Life WP updates - postponed to next week
  • Presentation from Oded Rotem about the DISCOVER model
    • Link to paper
    • They had difficulties understanding what needs to go in the RDF file
  • Uploaded&accepted models not shown in the zoo (Fynn and Esti take care of this)
  • (Joran): we are planning a full day of model upload (Jug lab + Open Calls). Who would be willing to be on a hotline support? We would fix a date
    • Jeremy will let them know once the new upload system is in a state to be tested
    • Then they will fix a date together
    • Great time to potentially try the new specs!

@oeway oeway mentioned this issue Feb 6, 2024
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@oeway
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oeway commented Feb 8, 2024 •
edited by FynnBe

February 7th 2024

Attendees

Name affiliation username (github)
Mariana Ferreira IGC @mariana-gferreira
Jeremy Metz KTH / Scilifelab @jmetz
Mehdi Seifi HT @mese79
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano
Anna Kreshuk EMBL @akreshuk
Arrate Muñoz UC3M @arratemunoz
Vera Galimova HT ??
Tomaz Vieira EMBL @Tomaz-Vieira
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Wei Ouyang KTH @oeway
Fynn Beuttenmüller EMBL @FynnBe

Agenda

@oeway
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oeway commented Feb 14, 2024 •
edited by FynnBe

February 14th 2024

Attendees

Name affiliation username (github)
Mariana Ferreira IGC @mariana-gferreira
Iván Hidalgo IGC @IvanHCenalmor
Jeremy Metz KTH / Scilifelab @jmetz
Mehdi Seifi HT @mese79
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano
Anna Kreshuk EMBL @akreshuk
Arrate Muñoz UC3M @arratemunoz
Vera Galimova HT ??
Tomaz Vieira EMBL ??
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Weize Xu KTH(visiting) @Nanguage
Fynn Beuttenmüller EMBL @FynnBe

Agenda

@oeway
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oeway commented Feb 21, 2024 •
edited by FynnBe

February 21th 2024

Attendees

Name affiliation username (github)
Mariana Ferreira IGC @mariana-gferreira
Iván Hidalgo IGC @IvanHCenalmor
Mehdi Seifi HT @mese79
Vera Galimova HT ??
Tomaz Vieira EMBL ??
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Weize Xu KTH(visiting) @Nanguage
Estibaliz Gómez de Mariscal IGC @esgomezm
Florian Jug HT @fjug
Wei Ouyang KTH @oeway
Fynn Beuttenmüller EMBL @FynnBe

Agenda

  • WP6 Open Challenges, presentation available here. @vera
  • Uploading all models from Open Call 1 to the BMZ format (in Heidelberg?)
  • Three projects from the OC to be in the Open Challenges:
    • Leaf segmentation challenge: Instance Segmentation + tracking for fine-tuning
    • Organelle Segmentation Challenge: 3D Segmentation of plankton cell (data not recieved yet)
    • Microscopy Denoising Challenge: 2D and 3D denoising tasks
  • Grand Challenge Platform
    • Data will be hosted on zenodo
    • Submissions in docker containers
    • Inference in AWS
  • Starting challenges at the end of March
  • Document with challenge organization info: here
  • Containers for testing the solutions and the correct format for the trained models to be in the zoo.
    • Documentation
    • Contianerisation methods (hello world container provided by the participant)
  • Relevant methods, make a list and motivate them to participate and create an updated leaderboard.
  • Wei: is it possible to ask the people to submit the models to the BioImage Model Zoo format?
  • Meetings about OC on fridays
  • Update on the new versoin of core: when? soon.
    • Also setting up the CI
  • Quick note on CC-BY(-*)
  • Hackathon in Heidelberg (March). Should there be a roadmap or agenda? (agenda)
    • In need for a title and a short abstract: everything we want to do around the model zoo.
  • Mini-hackathon and/or solvathon on May 6&7 2024.
    • EMBO Course 8th of May in Milano
    • Who wants to come?
    • Hackathon topics: WP6 Challenges and Open Calls or Workflows.
  • workflow related:

@cfusterbarcelo
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cfusterbarcelo commented Mar 6, 2024 •
edited by FynnBe

February 28th 2024

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Mariana Ferreira IGC @mariana-gferreira
Iván Hidalgo IGC @IvanHCenalmor
Mehdi Seifi HT @mese79
Vera Galimova HT ??
Tomaz Vieira EMBL ??
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Weize Xu KTH(visiting) @Nanguage
Estibaliz Gómez de Mariscal IGC @esgomezm
Joran Deschamps HT @jdeschamps
Jeremy Metz KTH @jmetz
Arrate Munoz-Barrutia UC3M @ArrateMunoz
Fynn Beuttenmüller EMBL @FynnBe

Agenda

  • WP7 presentation by Bea
  • BioImage.IO Chatbot updates
  • Euro-BioImaging Virtual Pub - this Friday!

@oeway
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oeway commented Mar 6, 2024

March 6th 2024

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Mariana Ferreira IGC @mariana-gferreira
Iván Hidalgo IGC @IvanHCenalmor
Tomaz Vieira EMBL @Tomaz-Vieira
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Estibaliz Gómez de Mariscal IGC @esgomezm
Joran Deschamps HT @jdeschamps
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano
Fynn Beuttenmüller EMBL @FynnBe
Constantin Pape Uni Göttingen @constantinpape
Weize Xu KTH(visiting) @Nanguage

Agenda

  • WP4 presentation - Containerisation
  • Hackathon in HD:
    • CellPose model, what's the issue?
  • What's the state of runnig the model online? --> It's working, refresh your browser!
  • BioEngine updates:
  • What's the status of next spec version? @Fynn
  • Small Open Calls and Challenges (WP6) hackathon in Milan (6th, 7th May), register
  • SPECS for workflows/bioengine apps/dl4miceverywhere notebooks: find a way to add conda environments (env.yamls or any other agreed format) into the rdf file so the same conda env can be called from all these software.

@cfusterbarcelo
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March 20th 2024

Attendees

Name affiliation username (github)
Wei Ouyang KTH @oeway
Mariana Ferreira IGC @mariana-gferreira
Iván Hidalgo IGC @IvanHCenalmor
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Fynn Beuttenmüller EMBL @FynnBe
Joran Deschamps HT @jdeschamps
Florian Jug HT @fjug.
Tomaz Vieira EMBL @Tomaz-Vieira
Weize Xu KTH(visiting) @Nanguage
Vera Galinova HT ??

Agenda

  • Schedule is empty: here
    • Anyone who is willing to present something, please add yourself there!
  • WP3 meeting happening tomorrow at 14:00h
    • Documentation rework >> first approach
    • June Hackathon (workshop + hackathon + uploathon)
  • Something about Heidelberg
  • Open Call Reviewers: Review! (new form link!!! see Bea last email)
  • New announcement channel on Element, post important news there! (e.g. "new documentation is out, please give feedback!")
  • Taking over maintenance of the uploader:
    • A dedicated room for this in Element is created
    • Increase bus factor for uploader maintenance
  • Move partner test scripts (only this for the moment) in GitHub to:
    • a) the bioimage-io organization
    • b) a new organization dedicated to it
    • c) 🏆 Only one repo in the bioimage-io organization
  • GTC Updates (Wei) GTC
    • They do care about life sciences and imaging
  • Move bioimageio packager to bioimage-io orga (it's in imjoy org now)

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March 27th 2024

Attendees

Name affiliation username (github)
Fynn Beuttenmüller EMBL @FynnBe
Wei Ouyang KTH @oeway
Florian Jug HT @fjug.
Joran Deschamps HT @jdeschamps
Mehdi Seifi HT @mese79
Vera Galinova HT ??
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano
Mariana Ferreira IGC @mariana-gferreira
Iván Hidalgo IGC @IvanHCenalmor

Agenda

  • Key Performance Inidicators (KPIs)

    • Number of models, notebooks, containers etc. in the BMZ
    • Number of total downloads
      • models
      • containers
      • notebooks
      • ...
    • BioEngine deployment instances > 5
    • Project numbers in the open call > xxx
    • Participants in the challenges > xxxxx
    • Hackathons and workshops participants
    • Publications and citations
      • Citations to the BMZ paper
      • Publications using a model from the BMZ
    • Users engaged in the help desks, forum, github issues
    • Community partner and model contributors
    • Time for the user upload a model
    • Count the number of cut edge (transformers) models that are in the BMZ
    • How much time does the answer an issue? (This can be not accurate because some of the GitHub issues are a recordatory or TODO remainders created by developers, not users asking for helps)

    TODO:

    • Track model test run number
    • Count the number of steps that takes to contribute a model

  • Free GPU power - under what circumstance do we want it or not?

    • What could we do with the GPU? Training, inference, running a container or running notebooks.
    • There is the problem that sometimes people is ocuppying a GPU but not using it because is working with the database.
    • Each dataset could be used in a different challenge and evaluate each model that can consume that challenge/dataset.
    • On the inference part, could it be interesting to have a link to a dataset to azure and consume them? The idea is to be able to consume any dataset if the user just has an azure link. Can this link be a problem for medical data? This can also be done on Zenodo, the difference is the downloading speed.

  • Download statistics

    • proposal: create a netlify download redirection service
    • it will redirect the download to s3 and send a tracking to Matamo

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April 03th 2024

Attendees

Name affiliation username (github)
Tomaz Vieira EMBL @Tomaz-Vieira
Anna Kreshuk EMBL @akreshuk
Mariana Ferreira IGC @mariana-gferreira
Iván Hidalgo IGC @IvanHCenalmor
Mehdi Seifi HT @mese79
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Fynn Beuttenmüller EMBL @FynnBe

Agenda

  • For the report two things need to be done:

    • Find some Key Performance Inidicators (KPIs).
    • Have quality assurance (or sanity check) of everything that is developed (eg. online uploader, local uploader GUI), someone apart from the developer should check it.

  • 2nd Open Calls are on the last step of being selected. After this, people will be contacted for consultation phase.

    • The Challenge is about to start soon (?). Waiting for the people who gave us the datasets and the uploading through zenodo (today or tomorrow) > summary: early next week the challenges will be announced.

  • June's Hackathon in Madrid will have the focus on some deliverable and will mix different PIs from other fields (like BiaPy). Monday and Tuesday is a Workshop and hands-on workshop (with students), and the last three days is the Hackathon.

  • The ChatBot is already available in the BioImage Model Zoo webpage. You need to register with an account. Wei is trying to reduce its access to avoid bots or unwanted interactions. Check new preprint here

  • Prerelease checks coordination: https://github.com/orgs/bioimage-io/projects/5

    • It is a project in GitHub's BioImage.IO organisation. There are different steps columns for in progres, under testing or released. Issues and PR can be linked and reviewers can be assigned.

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April 10th 2024

Attendees

Name affiliation username (github)
Tomaz Vieira EMBL @Tomaz-Vieira
Mariana Ferreira IGC @mariana-gferreira
Mehdi Seifi HT @mese79
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Fynn Beuttenmüller EMBL @FynnBe
Joran Deschamps HT @jdeschamps
Arrate Muñoz-Barrutia UC3M @arratemunoz
Wei Ouyang KTH @oeway
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano

Agenda

  • The Chatbot is now working (yes, now it is working not as las time when it was "working"). Test it here: https://bioimage.io/chat/
  • Google form to express interest (not registration yet!) to come to Madrid in June and give a Talk/Workshop.
    • Please do it before Friday!
    • We will send a registration link for the actual hackathon/uploathon soon! ^^
    • Organization:
      • 10th to the 14th of June in Madrid
      • 2 days workshops and talks (for students)
      • 3 days parallel hackathon and uploathon
  • BMZ Typeform question: "I am looking to quantify osteons from SEM images. I tested all the models in the zoo and didn't find any that were quite the right fit (of course). I wonder if you might be able to recommend one or provide some advice."
    • If there is a question on the typeform and there is no model available to segment those images... what do we do?
  • Status of the bioimage.io > are all models displayed?
    • no, not yet
  • ok with public list of reviewers? (emails)
    • we'll use github account ids with a mapping to names in the collection repo
  • EU-OpenScreen wondering what they should do to fill their PMs in AI4Life, should I put them in touch with WP7?
    • Yes! Kathy Skopelitou seems to be replacing Katja
  • Plan for the next deliverable for BioEngine

@oeway
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oeway commented Apr 17, 2024

April 10th 2024

Attendees

Name affiliation username (github)
Tomaz Vieira EMBL @Tomaz-Vieira
Mariana Ferreira IGC @mariana-gferreira
Mehdi Seifi HT @mese79
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Fynn Beuttenmüller EMBL @FynnBe
Joran Deschamps HT @jdeschamps
Arrate Muñoz-Barrutia UC3M @arratemunoz
Wei Ouyang KTH @oeway
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano

Agenda

  • The Chatbot is now working (yes, now it is working not as las time when it was "working").
  • Google form to express interest (not registration yet!) to come to Madrid in June and give a Talk/Workshop.
    • Please do it before Friday!
    • We will send a registration link for the actual hackathon/uploathon soon! ^^
    • Organization:
      • 10th to the 14th of June in Madrid
      • 2 days workshops and talks (for students)
      • 3 days parallel hackathon and uploathon
  • BMZ Typeform question: "I am looking to quantify osteons from SEM images. I tested all the models in the zoo and didn't find any that were quite the right fit (of course). I wonder if you might be able to recommend one or provide some advice."
    • If there is a question on the typeform and there is no model available to segment those images... what do we do?
  • Status of the bioimage.io > are all models displayed?
    • no, not yet
  • ok with public list of reviewers? (emails)
    • we'll use github account ids with a mapping to names in the collection repo
  • EU-OpenScreen wondering what they should do to fill their PMs in AI4Life, should I put them in touch with WP7?
    • Yes! Kathy Skopelitou seems to be replacing Katja
  • Plan for the next deliverable for BioEngine

@cfusterbarcelo
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April 17th 2024

Attendees

Name affiliation username (github)
Tomaz Vieira EMBL @Tomaz-Vieira
Mariana Ferreira IGC @mariana-gferreira
Mehdi Seifi HT @mese79
Fynn Beuttenmüller EMBL @FynnBe
Joran Deschamps HT @jdeschamps
Arrate Muñoz-Barrutia UC3M @arratemunoz
Wei Ouyang KTH @oeway
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano
Vera Galinova HT ??

Agenda

  • Model uploader, is it done? --> Urgent to plan next week's course

    • Jeremy is around finishing dev work.
    • https://github.com/bioimage-io/bioimageio-uploader-service
    • At the moment the netlify functions that served as a light backend before are being moved into the hypha service. Jeremy is actually doing this at the moment.
    • A basic uploading back up should be there again in a couple days

  • Bug in new models appearing in the website, is it solved? (Empanada models are under review)

    • MicroSAM models from Constantin are uploaded to the connection (Anna said it was smooth) but they are still not displayed in the website

  • Model retraining --> is there some toy code I could reuse for fine-tuning (out of the specs and bioimageio)

  • Paper resubmission?

    • Model upload
    • CI
      • bioimageio core is quite stable already so the notebooks can start being migrated

  • EBI course:

    • Anna gives the talk and shows the website (1h)

    • Dominik (1.15h)

    • Wei (30 mins) and Esti (1h) (after lunch)

    • Ask Dominik to switch the order (ESTI)

    • Ask craig to make more GPUs available for the test run to not collapse with Anna and the 40 participants (ESTI)

  • Bioengine HPC worker

    • Python package to install it
    • Then the user will be able to access their institutional HPC from the BioImage Model Zoo website and get new functionalities in the test run button. Basically this would support the use of local HPC from the browser.
    • It works with Singularity

@oeway oeway mentioned this issue Apr 25, 2024
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@cfusterbarcelo
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April 24th 2024

Attendees

Name affiliation username (github)
Mariana Ferreira IGC @mariana-gferreira
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Ivan Hidalgo IGC @IvanHCenalmor
Tomaz Vieira EMBL @Tomaz-Vieira

Agenda

  • Is there a meeting next week? We guess that there isn't.

  • WP4 meeting on the 2nd of April at 15:00 CEST.

@cfusterbarcelo
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May 8th 2024

Attendees

Name affiliation username (github)
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano

Agenda

  • Workshop & Hackathon/Uploathon in June in Madrid
    • Please, register in the form here as soon as possible.
    • Event webpage: here
    • Is the upload ready and documented?
    • Is there a list of models that we want to upload?

@cfusterbarcelo
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May 15th 2024

Attendees

Name affiliation username (github)
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Constantin Pape Uni Goettingen @constantinpape
Mariana Ferreira IGC @mariana-gferreira
Iván Hidalgo IGC @IvanHCenalmor
Wei Ouyang KTH @oeway
Nils Mechtel KTH @nilsmechtel
Fynn Beuttenmüller EMBL @FynnBe
Arrate Muñoz-Barrutia UC3M @arratemunoz

Agenda

  • [Caterina] Did you recieve my email as a reminder of this meeting yesterday?

    • Yes 😄

  • I2K Workshops:

    • Beginner BMZ (users): people who don't know BMZ and wants to learn about it and how to use it + chatbot for beginners - @anna
    • Advanced BMZ (developers): people who is interested on how BioEngine and core library works - @esti
    • BioImage.IO ChatBot (developers) - @caterina
    • DL4MicEverywhere - @esti

  • Workshop & Hackathon/Uploathon in June in Madrid

    • Please, register in the form here as soon as possible.
    • Event webpage: here

  • Uploathon:

    • Who is helping, the trainers
    • Is the upload ready?
    • Models to upload.
    • An idea from Anna: have a cool model such as Stardist, fine tune it in a new dataset, do some kind of competition on the best results, then the best one try to upload it to the BMZ (only uploading the best).

  • [Constantin] SAM Models in the zoo

    • Is it legal to rehost them?
    • Rough info on how to bring them into the zoo format?

  • [Constantin] Updating the zoo to new collection backend

  • [Constantin] Convenience functionality for prediction

  • [Constantin] How do I start a kaibu app (question for Wei, if there's time we can discuss, bringing it up here because its also something we should document at some point)

@cfusterbarcelo cfusterbarcelo self-assigned this May 21, 2024
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cfusterbarcelo commented May 21, 2024 •
edited

May 15th 2024

Attendees

Name affiliation username (github)
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Constantin Pape Uni Goettingen @constantinpape
Mariana Ferreira IGC @mariana-gferreira
Iván Hidalgo IGC @IvanHCenalmor
Wei Ouyang KTH @oeway
Nils Mechtel KTH @nilsmechtel
Fynn Beuttenmüller EMBL @FynnBe
Arrate Muñoz-Barrutia UC3M @arratemunoz

Agenda

  • [Caterina] Did you recieve my email as a reminder of this meeting yesterday?

    • Yes 😄

  • I2K Workshops:

    • Beginner BMZ (users): people who don't know BMZ and wants to learn about it and how to use it + chatbot for beginners - Anna and @cfusterbarcelo
    • Advanced BMZ (developers): people who is interested on how BioEngine and core library works - @esgomezm
    • BioImage.IO ChatBot (developers) - @cfusterbarcelo
    • DL4MicEverywhere - @esgomezm

  • Workshop & Hackathon/Uploathon in June in Madrid

    • Please, register in the form here as soon as possible.
    • Event webpage: here

  • Uploathon:

    • Who is helping, the trainers
    • Is the upload ready?
    • Models to upload.
    • An idea from Anna: have a cool model such as Stardist, fine tune it in a new dataset, do some kind of competition on the best results, then the best one try to upload it to the BMZ (only uploading the best).

  • [Constantin] SAM Models in the zoo

    • Is it legal to rehost them?
    • Rough info on how to bring them into the zoo format?

  • [Constantin] Updating the zoo to new collection backend

  • [Constantin] Convenience functionality for prediction

  • [Constantin] How do I start a kaibu app (question for Wei, if there's time we can discuss, bringing it up here because its also something we should document at some point)

@cfusterbarcelo
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May 22th 2024

Attendees

Name affiliation username (github)
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Mariana Ferreira IGC @mariana-gferreira
Iván Hidalgo IGC @IvanHCenalmor
Wei Ouyang KTH @oeway
Nils Mechtel KTH @nilsmechtel
Fynn Beuttenmüller EMBL @FynnBe
Mehdi Seifi HT @mese79
Estibaliz Gómez de Mariscal IGC @esgomezm
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano

Agenda

  • Help needed for the last consultation calls
  • Uploathon in Madrid (12th-14th June)
    • List of models - draft here
      • A CellPose model might be uploaded
      • I encourage all of you to edit and participate in this document to have a full list of models that might be interesting to upload doing the uploathon or in long-term.
    • Tomaz is doing a GUI to build the models there to get a zip and upload it in to the zoo. That's going to be very useful for the uploathon.
    • We (BMZ team) need to do a lot of testing on the upload process before the uploathon.
  • Last Call for Registering to the Hackathon in Madrid! Please, register here. We close the register this friday!
    • If someone of your group only wants to register for attending the workshop, register here.
  • Add to documentation rework spec documentation from here.

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May 29th 2024

Attendees

Name affiliation username (github)
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Mariana Ferreira IGC @mariana-gferreira
Iván Hidalgo IGC @IvanHCenalmor
Wei Ouyang KTH @oeway
Nils Mechtel KTH @nilsmechtel
Fynn Beuttenmüller EMBL @FynnBe
Mehdi Seifi HT @mese79
Estibaliz Gómez de Mariscal IGC @esgomezm
Beatriz Serrano-Solano Euro-BioImaging @beatrizserrano
Anna Kreshuk EMBL @akreshuk
Joran Deschamps HT @jdeschamps
Craig Russell EMBL-EBI @ctr26

Agenda

  • Internal Validation Workflow here

    • Motivation: recommendation to implement an internal way to release the small projects/components that we develop so we can all agree that the material is ready to go and report back.
    • It is important for internal testing! You can suggest reviewers if you want to point someone to test it.
    • People is encouraged to add their projects to the workflow. They can be added through issues and PR.
    • Who is a user of this board? People developing and releasing things and people interested in seeing the status of these small projects or components.

  • NEW DOCS! Visit them bioimage.io/docs!

    • Phase two: curate all the available documentation, add missing documentation and generally improve all the content.
    • Asking your contribution to update all the docs and add the missing documentation. Please give it a look!

  • Spec Docs (plan for improving the readability of the new version)

    • Readable version here - outdated
    • Also here - updated and generated automatically
    • And here - updated and generated automatically
    • Ideally: we should have an updated and automatically generated documentation human readable.

  • EBI S3 storage issue, download extremely slow: https://forum.image.sc/t/micro-sam-issues-in-napari-http/96750/9?u=oeway

  • Uploathon

    • Doc here
    • Any suggestion is encouraged!

  • Euro-BioImaging Annual report - updated factsheet

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cfusterbarcelo commented Jun 5, 2024 •
edited

June 5th 2024

Attendees

Name affiliation username (github)
Caterina Fuster-Barceló UC3M @cfusterbarcelo
Mariana Ferreira IGC @mariana-gferreira
Nils Mechtel KTH @nilsmechtel
Fynn Beuttenmüller EMBL @FynnBe
Mehdi Seifi HT @mese79
Vera Galinova HT ??

Agenda

  • Issues with the bioimage.io webpage @oeway
    • When clicking to a model and willing to access the source rdf file an error occours: image
    • Sometimes the webpage gets blocked while going from one card to another (don't know how to reproduce or when it happens exactly)
  • Uploader status
  • Models to upload.
    • From the OC.
      • Two Cellpose retrained models. Looking this notebook to see how they can be exported and uploaded to the zoo.
      • Some other models from students.
    • CellPose models.
      • Missing the post-processing.
    • PlantSeg.
      • It's on the way.
  • Uploathon two options:
    • Adapt ZeroCostDL4Mic notebook to the new specs - Mariana
    • Use BiaPy notebooks adapted to the new specs - Dani Franco
  • WP4 meeting tomorrow 6th June at 15:00h CET
  • Lisbon hackathon sign up

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