Micrograph Atlas Skill¶
Version 1.2.1 · Download the skill (micrograph-atlas) · CC0 · Disclaimer
In short
- An AI skill that gathers the cell micrographs scattered across the wiki into one page, the Microscope Atlas: genus, then cell shape, one row per organism.
- Why: side by side, cells can be compared; spread over journeys, organism pages and notes, they cannot.
- It curates only. Sizes come from the Dregs Analysis Skill, bench work from the Isolation Run Skill, and the wiki publishes the release bundle it builds.
- A busy field is cropped to the target cells with an arrow, never blurred or retouched. Commercial strains head each shape group; a bottle isolate sits under the one it resembles, a likeness, not an identification.
- It also keeps a shot list of what to photograph next.
- Start with How to install and use it.
Micrographs end up on many pages: journeys, organism pages, tasting notes, notes and guides. This skill gathers them into one page, the Microscope Atlas, so cells can be compared side by side: genus, then cell shape, then one row per organism with its thumbnails, sizes, conditions and every page that shows each photo. It is a gallery, not a primer. It curates; it never measures (the Dregs Analysis Skill does) and never runs a bench session (the Isolation Run Skill does). Everything here is experimental home practice: read the disclaimer first.
What it does¶
| Mode | Use it when | It does |
|---|---|---|
| Sync | Pages have changed, or a run has new micrographs | Scans the wiki for micrographs, compares them with the register and lists what is new, changed or gone, plus the micrographs the Isolation Run Skill flagged for the atlas; a page's own copy of an atlas image is recorded on the existing row, not as a new candidate |
| Classify | New organisms or photos to place | Proposes genus, shape group, forms and the commercial strain each isolate resembles, and which photos go in or stay out (with reasons); you confirm in a table |
| Prepare | A photo shows more than one organism, or is new | Has new photos measured by the Dregs Analysis Skill, crops to the target cells, adds arrows, conditions the files for the wiki and shows you a contact sheet |
| Build | The register and groups are confirmed | Writes the atlas page (opening with its In short card, from intro.md) and a release bundle from the register, the same bytes every time for the same inputs, and checks it |
| Gaps | Before a bench session | Lists what to photograph next: organisms with no usable micrograph, organisms with only unscaled photos, genera with none |
The register¶
One row per atlas image, in work/atlas/register.csv:
| Columns | Hold |
|---|---|
image_id |
ATL-001 and on: the register's own number, not a wiki ID |
published_file, backup_original, run_ref |
Where the image is: published file, original in the backup, isolation run and photo ID |
sources |
Every page that shows it; one image on several pages is one entry |
caption, alt, label |
Published caption and alt text, and the short caption under the thumbnail |
organism_id, strain, genus, shape_group, forms |
What it shows; forms lists every shape seen |
medium, days, temp_c, stain, contrast, magnification, camera_profile |
Conditions as recorded, "not recorded" otherwise |
scale, size_forms, length_um, width_um, diameter_um, n |
Sizes from calibrated measurements only, per cell form; otherwise "not to scale" |
work_src, derived_file, crop_box, arrows, edits |
How an atlas-owned file was made: source, crop, arrows (none, crop, crop+arrow) |
include, exclude_reason, confirmed |
Whether it goes in, why not, and when you confirmed it; only confirmed rows are published |
notes |
Assumptions, such as an assumed objective or an extrapolated scale |
Beside it: groups.yaml (the shape vocabulary, the groups, the anchors, one entry per organism
row and the approved group descriptions), intro.md (the page's "How to read this") and gaps.md
(the shot list).
Shapes, sizes and anchors¶
- Groups. Yeasts: round to ovoid, elongated or cylindrical, ogival or apiculate (pointed, lemon-shaped), pseudohyphal. Rods: short, long, filaments. Cocci: pairs, tetrads.
- Size first, shape second. Where cells are measured, the group follows the measured length and width; phone shots are grouped by shape and their length-to-width ratio alone, and say not to scale.
- Anchors. Commercial strains (WLP645, WLP648, Wyeast 5112 and so on) head the group they fall in. Bottle isolates sit under the anchor they resemble: a likeness, never an identification. An anchor without a photo shows "no photo yet" and leads the shot list.
- The organism is the unit. An isolate with two forms sits in its main group, with a note.
Crops and arrows¶
A field with more than one organism is never blurred or retouched. The skill crops to the target cells, from the backup original or the measured copy, and adds an arrow when other organisms remain in the crop. The caption says where it was cropped from and that arrows were added; the source page keeps the full field. A field that cannot be cropped to a clear target stays out, with the reason in the register. Dregs fields on opening, contamination demonstrations, banners and calibration shots stay out too, each with its reason.
How it works with the other skills¶
- Isolation Run flags each new micrograph in its photo register with the organism it shows and
an atlas flag (
candidate,no,done). At a milestone or when the journey closes it passes the candidates on; Sync lists them, and once they are in the register the run marks them done. - Dregs Analysis measures: Prepare asks it for dimension lines and sizes on calibrated photos and crops its measured copy. The atlas never re-measures.
- The wiki publishes. The skill delivers a release bundle (
manifest.yaml, the page body and the atlas's own images) ininbox/releases/micrograph-atlas-<date>/, never edits a page, and hands over with the bundle path, the gaps, review notes and open questions.
How to install and use it¶
- Download the zip, and the Dregs Analysis Skill for measuring.
- In Claude, install the skill by uploading the zip (Settings → Capabilities → Skills), or place
the folder where your Claude set-up reads skills.
scripts/atlas.pyneeds Python 3 with Pillow and PyYAML. - Start from
templates/groups.yamlandtemplates/intro.md, or ask for a first atlas: "Sync the atlas", then "Classify". Agree the groups and the inclusions at each checkpoint. - "Prepare the crops", look at the contact sheet, then "Build the atlas" and look at the preview.
- Before a bench session: "What should I shoot next?"
Without the author's wiki the register and page are files in the session's outputs, built from the micrographs you attach.
Changelog¶
| Version | Date | Change |
|---|---|---|
| 1.2.1 | 2026-11-08 | In short card in the intro template (wiki rules 0.37.0), taken as written by Build; Sync records a page's own copy of an atlas image on the existing row instead of a new candidate |
| 1.2 | 2026-11-08 | Page title "Brewing yeast and bacteria under the microscope" and a shorter summary for search (nav_title stays "Microscope Atlas"); the intro H1 matches. Includes 1.1 |
| 1.1 | 2026-11-07 | Not released on its own (included in 1.2). Sync no longer counts the atlas page as a source of its own photos; Build and Verify fail if the atlas lists or links itself; build --page-version, defaulting to the live page version with the minor part bumped; same-day re-release with build --out ...-2 |
| 1.0 | 2026-10-31 | First version: register, shape vocabulary with anchors, modes Sync, Classify, Prepare, Build and Gaps, crop-and-arrow rule, deterministic page and release bundle, candidates from the Isolation Run Skill, sizes from the Dregs Analysis Skill |