INVENTORY — what has actually been downloaded, and whether it can serve the 70 real images

Work package: REAL-SOURCES. Date: 2026-09-09. Requirement being tested against: 4096 x 2048 px PNG, gastric H&E, ~0.25 um/px (40x-objective equivalent), four categories.

The single test applied to every source below is: can it yield a 4096 x 2048 field at ~0.25 um/px without upscaling? A 4096 x 2048 field at 0.25 um/px covers a physical area of 1024 um x 512 um. A source therefore needs both:

1. a native sampling of about 0.25 um/px or finer, and
2. a field of view at least 1024 x 512 um wide.

Failing either one means the image can only reach 4096 x 2048 by interpolation, which invents detail that was never recorded. Nothing in this package is presented as native unless both tests pass.

A. Downloads found on Yash's Mac (from the Codex thread)

Source transcript read: [local]/rollout-2026-09-09T16-49-01-01a08636-eba7-7880-9173-546506ce7198.jsonl (589 JSONL records; user turns, assistant turns and tool calls extracted).

The thread covers four things: a hunt for the free full text of two papers, the GasHisSDB download and inspection, a broad dataset-landscape review, and a discussion of scraping Google Images / Wikipedia for H. pylori H&E with magnification captions. Only one image dataset was actually written to disk.

GasHisSDB counts, as verified locally in the prior package

(15 byte-identical duplicate files in the 80 px Normal group. Full inspection: operations/research/sgh-dataset-landscape-20260909/GASHISSDB-INSPECTION.md.)

The Google Images / Wikipedia route discussed in the thread

The thread's File:Stomach_helicobacter_he.JPG example was checked against the Commons API:

• 848 x 640 px, 77,439 bytes, CC BY-SA 3.0, by Commons user Alex_brollo, 2006.
• Its own description reads: "Gastric biopsy, H&E, 400x. Helicobacter pylori is barely visible inside mucus."

Reaching 4096 x 2048 from 848 x 640 is a 4.8x linear upscale, and the author states the organisms are barely visible even at native size. No files from this route were saved to disk — the thread discussed it and moved on. Nothing from Google Images exists locally to inventory.

Net result for section A: nothing Yash downloaded can supply a single one of the 70 images.

B. Material already staged on the IOFlood workbench

Container sgh-histopathology/workbench, under [local]/raw. Access: cd research/sgh-synthetic-histopathology && ./ioflood exec '<cmd>'.

B4 in detail — the only H. pylori-labelled H&E set we hold

(The directory is named hp-neu on the workbench. There is no dataset called "HP-Neu"; the NEU in the GitHub handle is Near East University, Nicosia. Correct name: the NEU H. pylori dataset.)

This is the dataset behind Ibrahim, Dirilenoğlu, Hacisalihoğlu, Ilhan & Mirzaei (2024), Classification of H. pylori Infection from Histopathological Images Using Deep Learning, Journal of Imaging Informatics in Medicine (DOI 10.1007/s10278-024-01021-0, open access via PMC11169399). 204 H&E images from 50 cases — so images within a case are correlated, as the authors themselves note. Filenames carry Sydney-system density grades (B129-19 HP (++).JPG, B198-19 HP (+++).JPG) — i.e. a pathologist did assert organism presence and density, which is exactly the label HiESD lacks.

It still cannot be used:

1. Resolution. 1280 x 960 is a 3.2x linear upscale short of 4096 x 2048. Even the three largest files at 2880 x 2048 are 1.42x short in width. There is no crop of any file that is natively 4096 x 2048.
2. Licence. CC BY-NC-ND 4.0. ND forbids distributing adapted material, and any crop, resample or format conversion is an adaptation. NC forbids commercial use. Submitting a derived image to a challenge is exactly the redistribution of adapted material that ND blocks. This is a hard stop independent of the resolution problem.

Its remaining value is as a reference for what H. pylori looks like in H&E and as an argument for writing to the authors — not as submission material.

C. New material staged by this package

C.1 Additional HiESD whole slides (downloaded to the workbench)

Chosen from the whole-collection yield survey (see SOURCES.md) to add slides that are strong on the two scarce categories (IM-only and IM-with-gastritis) and to widen the specimen pool beyond the 16 slides already held. Every file is under 2 GB; the whole batch is 4.83 GB.

Destination [local]/hiesd-wsi. Each was verified against figshare's published supplied_md5 after download.

Download ledger with the achieved md5 and byte count per file: [local]/dl.log on the workbench.

Reason recorded for downloading (per the package's own >2 GB rule — no single file exceeds 2 GB, and the batch total of 4.83 GB is recorded here for completeness): the 16 slides already held can supply the required field counts, but they are a small slice of the 104-slide collection and HiESD publishes no patient map, so specimen diversity in a 70-image submission would otherwise rest on an unverifiable assumption. These six slides roughly double the IM and IM+gastritis pool.

C.2 Wikimedia Commons micrographs (downloaded to the Mac, staged as candidates)

candidates/wikimedia-commons/ with provenance.csv. Fourteen files, all CC BY-SA 3.0 or 4.0. These are the best-resolution publicly licensed gastric H&E images that actually show H. pylori organisms. They are staged because they are the only real material we hold in which organisms are visible, and because the assessment of them is a required deliverable — not because they clear the resolution bar. Most do not. See SOURCES.md section 3 for the measurement and the verdict.

D. Summary verdict table

One source clears the bar for the geometry: HiESD. It does not carry an H. pylori label. That single sentence is the whole problem, and SOURCES.md sets out what to do about it.

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