docs: show how to open ARINA data with Show4DSTEM in Jupyter

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,40 +1,36 @@
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+### What problem does it solve?
 
+<!--
+Describe the concrete user or scientific-workflow problem. Explain why the
+change is needed; do not merely summarize the files that changed.
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-## Summary
+### What should reviewer(s) do?
 
-<!-- What does this PR change, and why? -->
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+Give reviewers a short, specific path through the important behavior, files,
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-## Verification
+### Verification
 
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 ## Core checklist (every PR)
 
 - [ ] The change includes focused tests for Python state/export behavior and
-  frontend build coverage where possible; start with `PYTHONPATH=src:. pytest -q`
+  frontend build coverage where possible; start with `PYTHONPATH=src pytest -q`
   and `npm run build`, or run `scripts/widget_local_signoff.sh`.
 - [ ] Before committing, inspect `git status --short` and `git diff --stat`;
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@@ -48,8 +44,9 @@ select any missing gates without relying on private logs.
   Saving a notebook after running widget cells stores that state silently;
   strip it before committing:
   `jq 'del(.metadata.widgets)' <nb>.ipynb > tmp && mv tmp <nb>.ipynb`
-- [ ] Only the sections below that this PR touches are kept; the rest are
-  deleted from this description.
+- [ ] Use every checklist item relevant to this PR. Keep the full checklist
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+  description.
 
 <details>
 <summary><b>Python API and docs</b> — new widget, loader, or API change</summary>
@@ -198,6 +195,7 @@ select any missing gates without relying on private logs.
   state. See [GitHub preview](https://github.com/electronmicroscopy/quantem.widget/blob/main/docs/github-preview.md).
 
 </details>
+-->
 
 ---
 

README.md

@@ -17,6 +17,10 @@ and 5D-STEM segmentation and clustering work
 ([paper](https://academic.oup.com/mam/article-abstract/32/3/ozag044/8701498))
 and the source data ([Zenodo](https://zenodo.org/records/18167694)).
 
+**[Start with the documentation](https://electronmicroscopy.github.io/quantem.widget/)**
+to load ARINA 4D-STEM data in Jupyter, open `Show4DSTEM`, and explore the
+interactive widgets.
+
 > `quantem.widget` is currently a prototype on
 > [TestPyPI](https://test.pypi.org/project/quantem-widget/) and is built on the
 > [`quantem`](https://github.com/electronmicroscopy/quantem) core.
@@ -31,39 +35,6 @@ pip install -i https://test.pypi.org/simple/ \
 See the [installation guide](https://electronmicroscopy.github.io/quantem.widget/install.html)
 for backend setup, Colab instructions, and verification.
 
-## Quick start
-
-Open an image or microscopy dataset without writing a notebook:
-
-```bash
-quantem show image.tif
-quantem show3d ./frames/
-quantem show4dstem ./masters/
-```
-
-Or construct widgets directly in Python:
-
-```python
-import numpy as np
-from quantem.widget import Show2D, Show4DSTEM
-
-Show2D(np.random.random((512, 512)))
-Show4DSTEM(np.random.random((64, 64, 128, 128)))
-```
-
-For real 4D-STEM data, load a master file onto the available GPU:
-
-```python
-from quantem.gpu.io import load
-from quantem.widget import Show4DSTEM
-
-Show4DSTEM(load("scan_master.h5"))
-```
-
-The [command-line guide](https://electronmicroscopy.github.io/quantem.widget/cli.html)
-and [tutorials](https://electronmicroscopy.github.io/quantem.widget/tutorials/download_data.html)
-cover data loading, HTML export, public example datasets, and complete workflows.
-
 ## Widgets
 
 | Widget | Use it for | Learn more |

docs/intro.md

@@ -13,24 +13,39 @@ and 5D-STEM segmentation and clustering work
 ([paper](https://academic.oup.com/mam/article-abstract/32/3/ozag044/8701498))
 and the source data ([Zenodo](https://zenodo.org/records/18167694)).
 
+## Start with ARINA 4D-STEM in Jupyter
+
+The demo above is the same `Show4DSTEM` workflow you can use at the microscope.
+After [installing](install), open a Jupyter notebook, load a completed ARINA
+`*_master.h5` file, and pass the result directly to the widget:
+
 ```python
 from quantem.gpu.io import load
-from quantem.widget import Show1D, Show2D, Show3D, Show3DSlices, Show4DSTEM, ShowPtycho, ShowEDS, ShowDiffraction, ShowFolder
+from quantem.widget import Show4DSTEM
+
+data = load("/data/session/scan_000_master.h5")
+viewer = Show4DSTEM(data)
+viewer
 ```
 
-## Quickest start: no notebook needed
+`load(...)` selects CUDA or Apple Metal automatically. Leave `viewer` as the
+final line, then move through scan positions or drag the detector to update the
+virtual image. Continue with the [Show4DSTEM tutorial](tutorials/show4dstem) or
+[Load and I/O](api/io).
+
+## Prefer the command line?
 
-After [installing](install), point the `quantem` command at a file or folder and
-it renders the right viewer in your browser:
+Point the `quantem` command at a file or folder when you want the same viewers
+without writing a notebook:
 
 ```bash
 quantem show2d image.tif         # an image            -> Show2D
 quantem show3d ./frames/         # a folder of frames  -> Show3D scrub
 quantem show4dstem ./masters/    # 4D-STEM master(s)   -> live viewer (or --html)
 ```
 
-It saves to `~/Downloads`, opens automatically, and picks the GPU (CUDA / Apple
-Metal) for you. Full details on [the command line](cli) page.
+It saves to `~/Downloads`, opens automatically, and picks the GPU for you. Full
+details are on [the command line](cli) page.
 
 ## Built for two platforms