Automated myelin annotation tool questions

Open
#30 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Domain
data

Research direction

Start with the automated myelin annotations and the myelin_auto_tags_2points table, using the supplied pt_root_id examples to reproduce the total, minimum, and maximum sheath-length results. Determine how the true/false pt_position and pt2_position combinations map to sheath presence, then compare that interpretation with the reported calculations. Done means the calculation or tag interpretation is explained and a concrete correction is identified.

Written by the indexing model from the issue text.

Description

Hi Microns team,

I am currently using the automated myelin annotations, included in the most recent release, to estimate the amount of myelin present on fully extended axons. Using the myelin quantification methods generated by Gamlin et al 2025, I've encountered some unexpected values derived from these annotations.

  1. A small subset of fully extended axons have more total myelin length than axon length, see examples below.
pt_root_id axon_path_length_um sum_sheath_um
864691135741655956 9854.10 162472.69
864691135118918109 10024.68 164995.78
864691135114295961 6734.73 109288.52
864691134886037498 16657.22 268364.24
864691135082864887 11892.34 189976.37
864691135066631492 11091.93 175369.10
864691134965778719 6717.52 103893.37
864691135409859785 10054.65 154407.81
864691135118298333 8382.66 126722.58
864691134887270650 11847.25 177253.62
864691136579919892 9684.50 138278.69
864691135375767369 6822.09 93702.23
864691136335553971 6775.12 92932.79
864691136619529179 7230.41 54893.46
  1. Calculating the minimum and maximum sheath length for many full extended axons results in some what implausible sheath length values. I've copied some examples below:
pt_root_id mean_sheath_um min_sheath_um max_sheath_um
864691135741655956 30.91 0.40 114.45
864691135118918109 30.97 1.96 126.60
864691135114295961 30.95 2.96 134.15
864691134886037498 29.08 1.14 139.63
864691135082864887 29.52 0.46 133.34
864691136664845278 1.57 1.57 1.57
864691135387529301 32.28 7.99 69.38

Do you have suggestions for how to best correct/improve these calculations?

It is also possible I am misunderstanding the myelin status designations in the myelin_auto_tags_2points table. How do the combination of true/false tags correspond to the presence or absence of a sheath? What would a pt_position = true and a pt2_position = false represent (or the inverse) for a myelin sheath?

Thanks for your help!

Dominant language
HTML
Stars
12
Forks
4
No merged PRs in 30d

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

More from AllenInstitute/microns_tutorial

All issues in AllenInstitute/microns_tutorial

Similar issues

More Data Engineering issues

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.