Add example notebook for DANDI:001933 (embargoed)

001933/DombeckLab/README.md

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+# DANDI:001933 — Dombeck Lab Fiber Photometry Notebook
+
+This notebook demonstrates how to access data from
+**[DANDI:001933](https://dandiarchive.org/dandiset/001933)**, a dataset of
+in vivo fiber photometry recordings of striatal dopamine release in awake,
+head-fixed mice expressing the dopamine sensor GRAB-DA3m.
+
+Two intersectional mouse lines targeting distinct dopamine neuron subtypes were
+studied: Anxa1-iCre mice (Anxa1+, vulnerable subtype) with fiber photometry in
+the dorsal lateral striatum (DLS), and Calb1-Cre mice (Calb1+, resilient subtype)
+with fiber photometry in the dorsal medial striatum (DMS). Optogenetic activation
+of subtype-specific dopamine neuron cell bodies in the substantia nigra pars
+compacta (SNc) was achieved via Cre-dependent ChRmine expression and red-light
+(635 nm) stimulation. LRRK2-WT and LRRK2-G2019S knockin mice were compared to
+investigate how pathogenic LRRK2 kinase activity affects dopamine synaptic function
+in a subtype-specific manner.
+
+> **Authentication required** — DANDI:001933 is currently embargoed.
+> A DANDI API key is required to stream data. Set it as an environment variable:
+> ```bash
+> export DANDI_API_KEY=your_key_here
+> ```
+> In Colab: add it via the Secrets panel (key icon on the left) under the name
+> `DANDI_API_KEY`.
+
+**Reference:** Chen, He et al. (in preparation)
+
+---
+
+## Notebooks
+
+### `001933_demo.ipynb`
+
+Streams a single session (subject 4007, Anxa-LRRK2-G2019S, 2025-08-13) from
+DANDI and demonstrates:
+
+1. NWBFile and subject metadata
+2. Fiber photometry metadata (`FiberPhotometryTable`, devices, indicator) via
+   [ndx-fiber-photometry](https://github.com/catalystneuro/ndx-fiber-photometry)
+   and [ndx-ophys-devices](https://github.com/catalystneuro/ndx-ophys-devices)
+3. Raw fiber photometry — full session and zoomed with stimulation epochs
+4. `CommandedVoltageSeries` — LED switching square wave (data provenance)
+5. Raw treadmill voltage (data provenance)
+6. Processed fiber photometry — baseline-corrected traces and ΔF/F
+7. ΔF/F aligned to a single stimulation onset
+8. Treadmill behavior (velocity and acceleration)
+9. Optogenetic epochs table — per-epoch power values and full-session power map
+10. Optogenetics metadata via [ndx-optogenetics](https://github.com/catalystneuro/ndx-optogenetics)
+11. Peri-stimulus ΔF/F (PSTH) — grand average, per-power traces, single-trial heatmap
+
+---
+
+## Installing the dependencies
+
+```bash
+git clone https://github.com/dandi/example-notebooks
+cd example-notebooks/001933/DombeckLab
+conda env create --file environment.yml
+conda activate dombeck_lab_001933
+```

001933/DombeckLab/environment.yml

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+name: dombeck_lab_001933
+channels:
+  - conda-forge
+dependencies:
+  - python==3.12
+  - pip
+  - pip:
+    - dandi
+    - jupyter
+    - h5py
+    - remfile
+    - pynwb
+    - numpy
+    - pandas
+    - matplotlib
+    - ndx-fiber-photometry>=0.2.3
+    - ndx-ophys-devices>=0.3.1
+    - ndx-optogenetics>=0.4.0