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Meeting 9 4 2020

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yoav freund edited this page Sep 4, 2020 · 13 revisions

Our next deadline is 9,10 Nov. Oversight meeting

Fixing previous problems

  1. Litao and Ed can now present the original structures on the corresponding brains in a way that resolves Beth's issue.
    • Beth to check all of the three foundation brain.
  2. Average atlas can be overlayed on any brain. needs aligning.
  3. Have shells created from masks for each of foundation brain. No average mask. No manually annotated and QA shells.

Documentation

  1. Ed should know how to redo what Litao and Kui know how to do.
  2. This Knowledge should be written as documentation on Github so that anybody can redo.
  3. Ability and Documentation to reconstruct annotation workflow.

Near-term Plan

  1. Obtaining data
  • Sexed matched pairs of complementary function. Priority is one sex matched pair.

1.a.

Pairings set #1 is Geneoglosis; Masseter; Phenic
Geneoglosis DK52 (F) - Done by Ed as of 26 Aug - Ch 1-3 HiRes ; need to verify overlays (Beth to make mtg w/Ed on 27 Aug - priority 1)
DK39 (M) - under Ed's resorting - soon to have Ch 2/3 HiRes; (Beth to make mtg w/Ed on 27 Aug)
Masseter DK54 (F) - need to correct for 6 µm sections; Beth and Hannah and David need to reasign sections; need to check Ch 2/3 HIRes - priority 2
DK43 (M) - need to correct for "squished" side + add Ch 2/3 HIRes (Beth to make mtg w/Ed on 27 Aug)

  1. Align section-to-section (local is Elastix on 32X rediced sectios extrapolated to full section - so long as sectios are OK)

    • [We are still working out the pipeline with CSHL/Bangalor.]

  2. In short term - align atlas manually ; DK and BF to do this for DK52 AFTER ED and BF verify sections and labeling

  3. Display overlay data (Ch 2 and 3) using Neuroglancer (27 Uag Mtg to clarify this)

  4. Access, display, and annotate DOTS! (labeled somata for now) - using neuroglancer.

  5. Assign each puncta an (x,y,z), and display in real units as a ball (same formal as with landmarks) in Neurglancer

Progress Table

Projection Animal sec2sec alnmnt 3 layers in neuroglancer atlas2sections alnmnt Mark dots display combined inslicer
Geneoglosis DK52 (F) done done Ready for dk and beth Beth working on it.
DK39 (M) done 9/5
Masseter DK54 (F) Not tiff yet.
DK43 (M) done

Other tasks

  1. Establish offsets for annotations to the three reference (Thionin) brains
  2. Simultaneous share and evaluate data across sites with Neuroglancer
  3. Add the shell of the brain

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