--- license: mit tags: - electron-microscopy - 4D-STEM - materials-science - quantem pretty_name: quantem-data --- # quantem-data **This page is in draft mode. We are still exploring the upload process and the `meta.json` template.** Keys, the checker, and these instructions will change as we try real pull requests. Use the current required keys for new PRs, and expect the template to grow. **This repo is currently used primarily by [quantem.widget**](https://github.com/electronmicroscopy/quantem.widget) (tutorial notebooks and `quantem.widget.datasets`). Other QuantEM packages may use it later. Public electron-microscopy data. MIT license. Downloads need no token. This page is the upload and download protocol. ## Download ```python from quantem.widget.datasets import show4dstem_gold ds = show4dstem_gold(size="small") ``` Notebook: [Example Data](https://github.com/electronmicroscopy/quantem.widget/blob/main/docs/tutorials/download_data.ipynb). ## Add data (Hugging Face pull request) Anyone with a Hugging Face account can add data. We follow a pull request process. Do not use `quantem.widget.io.upload`. Downloads need no token. Opening a pull request does. Create an account, then a token at [huggingface.co/settings/tokens](https://huggingface.co/settings/tokens). Use a **Write** token (classic). A **Read** token can download; it cannot open a PR. A fine-grained token also works if `--create-pr` is allowed on a public dataset. You do not need collaborator access to this repo. ```bash pip install huggingface_hub # skip if `hf` is already on PATH hf auth login ``` Paste the token. The prompt hides it. When asked `Add token as git credential? [y/N]`, answer `n`. `hf upload` reads `~/.cache/huggingface/token`. You do not need a git credential helper. Ignore any hint to run `git config --global credential.helper store`. ```bash hf auth whoami ``` That should print your username. If you already logged in with a Read token, run `hf auth login --force` and paste a Write token. If `--create-pr` returns 403 after a valid login, the token is Read or the fine-grained scopes omit Community PRs; make a Write token and login again. On SSH (no browser on that machine), paste a token. Do not use the browser login unless the browser and `hf` run on the same machine. Do not commit the token. A PR is the data file(s) plus one `meta.json`. Example already on the hub (2 files): ```text widget-tutorials/show4dstem/gold-512-bin4/full/data.npy widget-tutorials/show4dstem/gold-512-bin4/full/meta.json ``` One EMD: `gold_haadf.emd` + `meta.json` (2 files). A session folder: the `.emd` files + `meta.json`. Copy this `meta.json`. Required: `name`, `source`, `date`, `sample`, `shape`, `dtype`, `permission`. Optional: `sampling`, `units`, optics. Omit a key if unknown. Do not invent a number. `shape` is `[row, col]` for an image, `[frame, row, col]` for a stack, or `[scan_row, scan_col, det_row, det_col]` for 4D-STEM. `dtype` is the NumPy name of the stored array (or of the EMD image). Examples already on this repo: | Data | `shape` | `dtype` | | ------------------------- | -------------------- | -------- | | 2D HAADF (`gold-haadf`) | `[4096, 4096]` | `uint16` | | 4D-STEM (`gold-512-bin4`) | `[512, 512, 48, 48]` | `uint16` | | One EMD HAADF | `[4096, 4096]` | `uint16` | Processed float data uses `"float32"`. Read both values from the file (`arr.shape`, `arr.dtype`, or the EMD image) and copy them into `meta.json`. ```json { "name": "gold_512_npy_bin4", "source": "Arina 4D-STEM, Nano Titan, session 20260423, gold_004_master.h5", "date": "2026-04-23", "sample": "gold nanoparticles", "shape": [512, 512, 48, 48], "dtype": "uint16", "permission": { "received": true, "from": ["Sangjoon Lee"], "collectors": ["Sangjoon Lee"], "date": "2026-04-23" }, "sampling": [0.5, 0.5, 1.84, 1.84], "units": ["A", "A", "mrad", "mrad"], "voltage_kV": 300, "semiangle_mrad": 30, "camera_length_mm": 91 } ``` `source` is microscope, facility, and original file. `date` is acquisition day (`YYYY-MM-DD`). `permission.received` must be `true`. `from` is who granted the share (one name or several). `collectors` is who used the instrument (one name or several). `permission.date` is when that share was granted. ```bash python -m check_meta ./gold-512-bin4 hf upload bobleesj/quantem-data ./gold-512-bin4 \ widget-tutorials/show4dstem/gold-512-bin4/full \ --repo-type dataset --create-pr ``` Run `python -m check_meta` from a checkout of this dataset so the `check_meta/` package is importable. `./gold-512-bin4` is your local folder (`data.npy` + `meta.json`). The last `hf upload` path is the folder on this repo. The hub path is `widget-tutorials////`. For a new ShowBragg set that would be `widget-tutorials/showbragg//full`. Size is `small`, `medium`, `large`, or `full`. Use `widget-tutorials/shared/` only when more than one widget will read the same files. `python -m check_meta` must print `ok` or do not open the PR. Resume a stopped upload with `--revision refs/pr/N` (do not pass `--create-pr` again). Merge is on the [Community tab](https://huggingface.co/datasets/bobleesj/quantem-data/discussions). ### Coding agents A coding agent can open the Community pull request. The human creates the Write token and attests permission. The agent does not invent `permission.*`, `sampling`, or optics. The agent does not run `hf auth login` (that prompt is interactive). The agent does not write the token into a repository file. ```bash # human already ran `hf auth login` or exported HF_TOKEN (Write) hf auth whoami hf download bobleesj/quantem-data --repo-type dataset \ --include "check_meta/**" --include "templates/meta.json" \ --local-dir ./quantem-data-tools export PYTHONPATH="$PWD/quantem-data-tools${PYTHONPATH:+:$PYTHONPATH}" python -m check_meta ./gold-512-bin4 hf upload bobleesj/quantem-data ./gold-512-bin4 \ widget-tutorials/show4dstem/gold-512-bin4/full \ --repo-type dataset --create-pr \ --commit-message "add show4dstem gold-512-bin4 full tutorial data" ``` `hf auth whoami` must print a username. If it fails or `--create-pr` returns 403, stop and ask the human for a Write token (`export HF_TOKEN=...`). If `python -m check_meta` is not `ok`, stop. After the upload, give the human the Community URL. Do not merge. Copyable widget prompt: [Add tutorial data](https://github.com/electronmicroscopy/quantem.widget/blob/main/docs/agent-prompts.md#add-tutorial-data-hugging-face-pull-request). If a notebook should call `quantem.widget.datasets`, open a GitHub PR after this one merges: [Contribute tutorial data](https://github.com/electronmicroscopy/quantem.widget/blob/main/docs/tutorials/contribute_data.md). Colab: [Show4DSTEM](https://colab.research.google.com/gist/bobleesj/54864ce5b2a6f0a4fd5ae1e5d5719b45/show4dstem_colab.ipynb) · [Workshop v1](https://colab.research.google.com/gist/bobleesj/a05a90185c6cddbb331342cae6d7e9c1/berk_workshop_v1.ipynb) ## Acquisition parameters The 20260423 drift session optics are confirmed via the session HAADF EMD. 4D-STEM `scan_sampling` is an operator pattern from a sibling SSB session. | dataset | voltage | probe | CL | scan | scan sampling | det pitch | mag | | -------------------------------- | -------- | --------- | ------- | ----------- | -------------- | ------------ | ----------- | | `haadf/gold_haadf_npy` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 4096² image | 0.0186 nm/px | n/a | FOV 76.2 nm | | `4dstem/gold_512_npy_bin8` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 512² | 0.5 Å (op) | 3.68 mrad/px | unknown | | `4dstem/gold_512_npy_bin4` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 512² | 0.5 Å (op) | 1.84 mrad/px | unknown | | `4dstem/gold_512` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 512² | 0.5 Å (op) | 0.46 mrad/px | unknown | | `4dstem/gold_30mrad1.3mx04`…`09` | 300 kV | 30 mrad | 91 mm | smaller | (session yaml) | 0.46 mrad/px | 1.3 Mx | | `haadf/gold_haadf.emd` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 4096² image | 0.0186 nm/px | n/a | FOV 76.2 nm | ✓ = confirmed via EMD/yaml. `(op)` = operator pattern, not file-certified. ## License Files on this repo are published under **MIT**. **You must have explicit written permission from the person who collected the data before you open a pull request**, unless you collected the data yourself. Put that receipt in `meta.json` (`permission.received`, `permission.from`, `permission.collectors`, `permission.date`). If you collected it yourself, set `from` and `collectors` to your name. Do not open a pull request without that permission. `python -m check_meta` must print `ok`.