WG meetings 2024 - mesoscope/cellpack GitHub Wiki

June 11th, 2024

Updates and agenda

  1. PR for loading grid files from s3: need get it to work with firebase upload
  2. SAC is over
  3. Discussed grid file paths

TODO:

  1. upload grid file path to firebase on upload
  2. need a second approval on open PR
  3. revisit upload algorithm (debug)
  4. refactor cellpack analysis repo, and do packing with more variation: a more faithful version of the distribution

May 28th, 2024

Updates and agenda

  1. the slides for SAC are done
  2. plots for cellpack results in simularium file is working
  3. two prs for cleanup
  4. https links work for loading meshes from s3
  5. merged github action cache so the actions run faster

TODO (next meeting):

  1. discuss feasibility of uploading a whole bunch of recipes
  2. discuss grid file paths in firebase?

May 14th, 2024

Updates and agenda

  1. SAC writeup and slides
  2. Loading meshes from s3 does not work - will need to update MeshStore.get_mesh_filepath_and_extension(filename)
  3. github action cache - discuss upgrading to pyproject.toml and python 3.10
  4. discuss cleaning up unused recipes and config options from repo
  5. if time: discuss questions from the previous server chat

Notes

  1. Use https:// link instead of s3 URIs for loading meshes from s3

Action Items:

  1. Saurabh: loading grid files from s3
  2. Ruge: add plots to result files
  3. Saurabh: check priority packing (removed functions included some priority calculations) and other functions moved to utils.py. Get rid of unused code completely and move older analyses to the cellpack-analysis repository.
  4. Saurabh: test pdm build backend to manage dependencies, will need to update test workflows as well
  5. Megan: do a first pass of the cellPACK 1 page summary
  6. Saurabh: Incorporate edits from Megan and Graham into cellPACK 1 page summary

April 30th, 2024

Updates

  1. Presented at cell morph WGF meeting on 25th April
  2. Saurabh was able to upload and run a peroxisome recipe through firebase
  3. Lunch meeting presentation prep

TODO:

  1. Saurabh: test loading meshes from s3
  2. Saurabh: loading grid files from s3
  3. Saurabh: look at Ruge's PR

April 16th, 2024

Updates

  1. Completed: Normalize obtained nuclear distance distribution with the available space to see if we recover a flat line
  2. Progress in analysis pipeline
    • Question around using firebase:
      • first need to upload local recipes using the upload script
      • also possible to run a json from AWS? worth pursuing?
  3. Ruge has open PR for skipping db system in the case that a user is only doing local packing
  4. last presentation April 9: available space investigations
  5. Proposal for cellPACK server (talk about more today?)

TODO:

  1. for normalized distribution: 300 cells data pooled together. Try doing it per cell and then plot ratio
  2. ideas: two theories for the observed plot ratio: is it just excluded space? Ie the ER is keeping the peroxisomes from being close to the nucleus? or do they actually have a preference for the edge of ER

April 2nd, 2024

Updates

  1. Discussion on grid point selection for biased packings

TODO:

  1. compare distance distributions across elongation shape mode bins

  2. Normalize obtained nuclear distance distribution with the available space to see if we recover a flat line

    a. Can also be used as a test for deviation from randomness

  3. Use z position as a metric to look at endosome distribution

March 19th, 2024

Updates

  1. Set up meeting with Alli re: cellPACK server on 20th March
  2. Merged PR 224, 237
  3. Firebase packing path updates
  4. Published a new version on PyPI
  5. removed cvapipe analysis dependency from the cellpack-analysis repo
  6. Presented updates at the scientific simulations WG - punctate analysis on observed peroxisome data

TODO:

  1. Saurabh: review PR #230
  2. Saurabh/Karthik: Install cellPACK from PyPI in the cellpack-analysis repository
  3. Lunch meeting updates on April 17th - Follow up and outline on 2nd March
  4. Ruge: issue #238

March 5th, 2024

Updates

  1. Presented at BPS
  2. Started cellpack infrastructure meetings (pipeline optimization/tooling)
  3. generated synthetic data for representation learning group

TODO:

  1. talk to Alli (working with Ruge to make a cellpack server)

Feb 2nd, 2024

Updates

  1. removed panda3d (in review)
  2. Met with Jessica to discuss pipeline optimization/tooling, going to have an ongoing meeting to coordinate efforts

TODO:

  1. Path validation PR to open
  2. PR comment
  3. see if we can take a cellMorph meeting after BPS to have Julie see new data

Jan 26th, 2024

Updates

  1. fixed issue with surface packing
  2. Reviewed open gradient image PR (still needs second review, and requested one small change)
  3. Started reading staging firebase setup PR, but need to finish review

TODO:

  1. remove panda3d
  2. start on some issues towards making cellpack usable by other people

Jan 19th, 2024

Update

  1. we work on #213 but didn't finish, some meshes seem to not be loading correctly
  2. Worked on exploring the baseline/null hypothesis of packing many replicates and running the analysis on the set to see what we can define as "same" in our system.
  3. In review: staging firebase setup

TODO:

  1. some known speed ups (#219)
  2. PR review (saving gradient data as image)
  3. #212: firebase validation and deleting metadata