docs: slim card to provenance + one pointer to quantem.widget docs, license MIT
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README.md
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license:
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tags:
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- electron-microscopy
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- 4D-STEM
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# quantem-data
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Reference electron-microscopy datasets
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- **`haadf/`** — HAADF survey images. `_npy` variants are pre-cooked NumPy + a `meta.json` sidecar carrying sampling + optics; the originals are full Velox EMD files.
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A ready-to-run notebook sits at `notebooks/show4dstem_colab.ipynb` in this repo.
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## One-click workshop notebook (Google Colab)
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[](https://colab.research.google.com/gist/bobleesj/54864ce5b2a6f0a4fd5ae1e5d5719b45/show4dstem_colab.ipynb)
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It does the full pipeline in 7 cells: install `quantem.widget` (TestPyPI rc) + `quantem` (dev fork branch), download the pre-binned NumPy bundle from this dataset, wrap it as `Dataset4dstem.from_tensor`, render with `Show4DSTEM` in your browser via WebGPU. No CUDA on Colab. No quantem.live.
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[](https://colab.research.google.com/gist/bobleesj/a05a90185c6cddbb331342cae6d7e9c1/berk_workshop_v1.ipynb)
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**Workshop v1** — real gold 4D-STEM: browse + bright field + dark field + probe + DPC, all on the Colab T4. No `quantem.live`, no local install. The notebook lives at `notebooks/berk_workshop_v1.ipynb` in this repo and on the `berk-workshop` branch of `bobleesj/quantem`.
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## Workshop quick start — Show4DSTEM (any Jupyter)
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```python
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!pip install -q --pre --extra-index-url https://test.pypi.org/simple/ quantem.widget huggingface_hub
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!pip install -q git+https://github.com/electronmicroscopy/quantem.git@dev
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import os, json, numpy as np, torch
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from huggingface_hub import snapshot_download
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from quantem.core.datastructures import Dataset4dstem
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from quantem.widget import Show4DSTEM
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allow_patterns=["4dstem/gold_512_npy_bin8/*"])
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asset = os.path.join(folder, "4dstem", "gold_512_npy_bin8")
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data = np.load(os.path.join(asset, "data.npy"))
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meta = json.load(open(os.path.join(asset, "meta.json")))
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dset = Dataset4dstem.from_tensor(torch.from_numpy(data),
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sampling=meta["sampling"], units=meta["units"])
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Show4DSTEM(dset)
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```
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``
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from huggingface_hub import snapshot_download
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from quantem.widget import Show2D
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folder = snapshot_download("bobleesj/quantem-data", repo_type="dataset",
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allow_patterns=["haadf/gold_haadf_npy/*"])
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asset = os.path.join(folder, "haadf", "gold_haadf_npy")
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img = np.load(os.path.join(asset, "data.npy"))
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meta = json.load(open(os.path.join(asset, "meta.json")))
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## Acquisition parameters
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The 20260423 drift session's optics are **confirmed via the session's own
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| dataset | voltage | probe | CL | scan | scan sampling | det pitch | mag |
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✓ = confirmed via EMD/yaml. `(op)` = operator pattern, not file-certified.
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##
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| name | kind | shape | dtype | size | use |
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| `4dstem/gold_512_npy_bin8/` | NumPy bundle | (512, 512, 24, 24) | uint16 | ~302 MB | workshop / Colab demo |
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| `4dstem/gold_512_npy_bin4/` | NumPy bundle | (512, 512, 48, 48) | uint16 | ~1.2 GB | sharper workshop version |
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| `4dstem/gold_512/` | Arina h5 | (512, 512, 192, 192) | uint16 | ~5 GB | power user |
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| `4dstem/gold_30mrad1.3mx04` … `09` | Arina h5 | varies | uint16 | ~5 GB each | series demo |
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| `haadf/gold_haadf_npy/` | NumPy bundle | (4096, 4096) | uint16 | ~34 MB | workshop / Colab Show2D |
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| `haadf/gold_haadf.emd` | Velox EMD | (4096, 4096) | uint16 | a few MB | full optics carrier |
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Each `_npy*` bundle ships a `meta.json` next to `data.npy`: shape, dtype, sampling, units, voltage / probe / CL (with provenance flags) when known.
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## Power-user path (full data, GPU decompression)
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Got an NVIDIA GPU and want the full Arina h5 / Velox EMD path? Install [`quantem.live`](https://github.com/bobleesj/quantem.live):
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```python
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from quantem.live import io
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from quantem.widget import Show4DSTEM, Show2D
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import torch
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folder = io.download("gold_512")
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result = io.load(io.discover_masters(folder)[0], det_bin=2)
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Show4DSTEM(torch.from_dlpack(result.data))
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ds = io.read_image(io.download("gold_haadf"))
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Show2D(ds)
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```
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## Memory (VRAM) for the full h5
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| `det_bin` | detector | loaded | peak VRAM | fits 16 GB? |
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| 1 | 192×192 | 18 GB | ~25 GB | no |
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| **2** | 96×96 | 4.5 GB | **~6.9 GB** | **yes** |
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| 4 | 48×48 | 1.1 GB | ~2.2 GB | yes |
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| 8 | 24×24 | 0.3 GB | ~0.5 GB | yes |
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## Licence
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---
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license: mit
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tags:
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- electron-microscopy
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- 4D-STEM
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# quantem-data
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Reference electron-microscopy datasets (gold 4D-STEM and HAADF) for browsing
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and learning with [quantem.widget](https://github.com/bobleesj/quantem.widget).
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This repo just hosts the data — all instructions live in one place:
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**How to download and use this data:** follow the
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[Download data tutorial](https://bobleesj.github.io/quantem.widget/tutorials/download_data.html)
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in the quantem.widget docs. One call per dataset:
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```python
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from quantem.widget import Show4DSTEM
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from quantem.widget.datasets import show4dstem_gold
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Show4DSTEM(show4dstem_gold())
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```
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Layout: `4dstem/` holds Arina h5 originals plus pre-binned `_npy_bin*` NumPy
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bundles; `haadf/` holds Velox EMD originals plus `_npy` bundles. Every `_npy*`
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bundle ships a `meta.json` (shape, dtype, sampling, units, optics) next to
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`data.npy`.
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Workshop notebooks (Google Colab, no local install):
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[Show4DSTEM demo](https://colab.research.google.com/gist/bobleesj/54864ce5b2a6f0a4fd5ae1e5d5719b45/show4dstem_colab.ipynb)
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·
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[Workshop v1](https://colab.research.google.com/gist/bobleesj/a05a90185c6cddbb331342cae6d7e9c1/berk_workshop_v1.ipynb)
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## Acquisition parameters
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The 20260423 drift session's optics are **confirmed via the session's own
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HAADF EMD** (`AccelerationVoltage`, `BeamConvergence`, `CameraLength`).
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4D-STEM `scan_sampling` is an **operator pattern from a sibling SSB session**
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— the drift acquisition itself was never per-file calibrated.
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| dataset | voltage | probe | CL | scan | scan sampling | det pitch | mag |
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✓ = confirmed via EMD/yaml. `(op)` = operator pattern, not file-certified.
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## License
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MIT — free to use for anything. Citing
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[quantem.widget](https://github.com/bobleesj/quantem.widget) in publications
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is appreciated.
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