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# System prepended metadata

title: IDR-NGFF 2020-W48
tags: [NGFF]

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---
tags: NGFF
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# IDR-NGFF 2020-W48

## 2020-11-26
- Josh:
  - social media on ngff repo
  - then there's the question of v0.2 have a few days to figure that out
- Will:
  - labels CLI PR to look at.
  - playing with napari to stitch a plate
    - did get it working locally (2D) with zoom-in
    - tricky to get it working with s3.
- Seb:
  - HCS is good for review
  - one PR open for `acquisitions: []` fix
  - regenerating data today, complete list on idr-zarr1-dev
    - will try the same with bioformats2raw to compare
- David
  - S3 rabbit hole ... Works for David but not for Josh.
  - qupath doesn't look to handle multi-filesets well
- Petr:
  - outreach in Goteborg, 8:10 UK
    - miss standup
    - need helper (also to miss standup)
      - 2 hours with 20min break
      - ends 1030 UK time.
    - not J-m
    - need a buffer since there's been 

## 2020-11-25
- Josh:
  - NGFF & bikeshed (from standup). Any comments?
  - Merge all PRs into 'latest'. 
- David:
  - ZarrReader: weird dependency issue when bundled into a single jar with S3. Fine in fiji but not CLI. Just ome-commons causes the issue.
    - Josh: may be ok to build an unbundled jar
    - David: see uncommented section
  - Testing in QuPath...
- Petr: preparing workshop feed
  - How granular? Single I2K entry
  - Seb: switching to GHA for quick review
- Seb
  - working on latest HCS update (bikeshed experience)
  - cf. bioformats2raw etc. from Melissa
  - naming
    - Latest == in-progress
    - 0.1 == last release
    - Will: are we going to 0.2?
    - Josh: 0.2-dev? 0.2-rc1? Requires copying latest/index.bs to NEWDIR/index.bs
    - Will: may depend on how much we show HCS. Not sure how much people are interested. People aren't likely to start working with many images at one time.
    - Seb: HCS brings us the concept of "batch", first example of a spec that's a collection of images. Eventually, everyone wants that.
    - Josh: esp. with the label overlay
    - Petr: if you show just one image, then the questions come: "where are the others?", "what about looping?"
- Will/I2K:
  - If we're going to show HCS, then we should have things merged.
    - Agreed, to spec latest but actually 0.2 (or similar) then merge PRs and tag.
  - FYI: https://github.com/ome/omero-guide-python/pull/27  more details on layout
  - Finishing up PRs.
  - Notebooks for showing analysis? Not really. More how to get a numpy array.
  - Will: Notebooks local?
    - Petr: mybinder requires caution (trick was: leave zoom, restart page, ... 5 min of debugging)
      - Simon: 5 minutes is probably the critical bit.
    - Petr: repo2docker doesn't work on Windows
    - Simon: load on mybinder before the workshop
    - Petr: but have redundancy locally in case it fails
      - Will: was using vizarr example with `pip install` and `jupyter notebook` (*not* repo2docker)
      - Petr: conda -> pip install repo2docker works. (Once it was necessary to install from master)
- Josh/I2K
  - email with instructions: 
  - image.sc meeting
  - image.sc HCS (if we get to 0.2)

## 2020-11-24
- Josh: 
  - biorxiv paper on image.sc (N5 plugin). N5-N5 format (Combining bdv.xml + n5). Janelia COSEM
  - At minimum, helps with spatial context.
  - Fixing Python 3.9, then back to PR testing
  - Also, PPTXing
- Will:
  - starting to think about what to show for i2k
    - what can be hands-on
      - actively code?
      - mixture of people: python, java, javascript, non-coders
      - Will: was imaginging zarrlite.js. play with parameters, render a plane. likely the simplest implementation.. likely the simplest implementation.. likely the simplest implementation.
        - instructions for installing
        - Petr: depends on who is coming
        - Will: imagine _most_ want to learn _something_ (even if just imagej macros)
        - Petr: don't want to give 18 the feeling they aren't welcome
        - Josh: breakout rooms? Petr: available?
    - what do we want them to understand
    - PRs
      - vizarr
        - Will: merge conflict (various dependencies)
        - Josh: want to move code to S3. would like to have it merged.
- switching to https://hackmd.io/qmr2e48-QaqFlXNuMc-Fmw

## 2020-11-23
- JRS:
  - Will's links work better on Campus
    - Demoable. Make video at school?
    - Josh: warn everyone in terms of bandwidth boundaries.
  - Small list of fixes for usability
    - e.g. if you change the rendering at one level, the rendering isn't passed to the next level. i.e. be prepared to hear about them.
- Will/I2K
  - choosing people. Several at level one? Seb: yes (20 is crazy)
  - how many? 10-20? 130 applicants. 40 at 1st.
  - Petr: prepare exercises or no hands-on (for this time length)
  - Will: could update local code to read pixels from ome-zarr
  - Simon: what do we want?
    - Josh: hope to get 2-3 people to engage after the workshop
    - Will: take a large number of people, but nothing interactive
- David
  - hopefully solving multiscale issue today
- Petr
  - who was the audience for Friday? (seemed sub-optimal)
  - Josh: think for visualization it's clear. For analysis it's difficult.
  - Petr: perhaps only for batch analysis, but ilastik is not an easy beast.