---
pretty_name: "PFNC GST HAADF-STEM/EDS Tomography — b2_d3"
license: cc-by-nc-nd-4.0
tags:
- electron-microscopy
- electron-tomography
- stem
- haadf
- eds
- edx
- spectrum-imaging
- materials-science
- semiconductor
- phase-change-memory
- gst
- limited-angle-tomography
size_categories:
- n<1K
---

# PFNC GST HAADF-STEM/EDS Tomography — Lamella `b2_d3`

## Dataset summary

This dataset contains a limited-angle, multi-frame HAADF-STEM and EDS electron-tomography acquisition of a cross-sectional Ge-Sb-Te phase-change-memory lamella.

The data were acquired on a **Thermo Fisher Scientific Titan Themis** at the **Platform for Nanocharacterisation (PFNC), CEA Grenoble**, operated at **200 kV** and equipped with a four-detector **Super-X EDS** system.

The original lamella identifier is:

```text
b2_d3
```

The mapping of this lamella to the virgin or SET device described in the associated publication remains to be confirmed.

The dataset preserves:

- 16 original Velox EMD acquisition containers;
- 50 HAADF frames at each retained tilt;
- a 50-frame EDS spectrum stream at each retained tilt;
- integrated spectra and embedded elemental net-intensity maps;
- extracted HAADF and elemental tilt-series stacks;
- an aligned HAADF tilt series;
- per-projection pixel shifts referenced to the 0° acquisition;
- an explicit tilt-angle list.

## Dataset name

Recommended public title:

```text
PFNC GST HAADF-STEM/EDS Tomography — Lamella b2_d3
```

Recommended Hugging Face repository slug:

```text
pfnc-gst-haadf-stem-eds-tomography-b2-d3
```

This name identifies the facility context, material system, acquisition modalities, tomography task, and original lamella identifier without making an unverified claim about the device state.

## Provenance and credits

| Role | Person |
|---|---|
| Original acquisition operator | Le-Duc Minh Tran — `le-ducminh.tran@cea.fr` |
| Dataset curator | Daniele Picone — `daniele.picone@cea.fr` |
| Scientific contact | Daniel Del Pozo Bueno — `daniel.delpozobueno@cea.fr` |
| PFNC contact | Zineb Saghi — `zineb.saghi@cea.fr` |
| Dataset organization | CEA-Leti, Grenoble |
| Acquisition facility | PFNC, CEA Grenoble |

## Instrument and acquisition

| Field | Value |
|---|---|
| Facility | Platform for Nanocharacterisation (PFNC), CEA Grenoble |
| Microscope | Thermo Fisher Scientific Titan Themis |
| Exact commercial generation/submodel | Not documented |
| Operating voltage | 200 kV |
| Corrector | Probe corrector |
| EDS system | Super-X, four silicon-drift detectors |
| Embedded detector identifier | `SuperXG1` |
| Acquisition software | Velox |
| Embedded Velox version | `3.17.0.967-b5399cab` |
| EMD format | Velox EMD version 11 |
| Acquisition date | 2025-07-07 |
| Beam current | 115 pA |
| Camera length | 110 mm |
| Pixel size | 10.67 Å/pixel |
| Frame size | 400 × 300 pixels |
| Dwell time | 40 µs |
| Frames per retained tilt | 50 |
| Time per frame | 5.57 s |
| Cumulative acquisition time per tilt | 278.5 s |
| Fluence per frame | 2.52 × 10² e⁻ Å⁻² |
| Fluence per tilt | 1.26 × 10⁴ e⁻ Å⁻² |
| Approximate total fluence | 2.0 × 10⁵ e⁻ Å⁻² |

## Sample

| Field | Value |
|---|---|
| Lamella identifier | `b2_d3` |
| Filename identifier | `D3` |
| Material system | Ge-Sb-Te phase-change-memory device |
| Specimen form | Cross-sectional FIB lamella |
| Operational state | Unknown: virgin or SET |
| Approximate GST-region thickness | 50 nm, as reported for the associated study |
| Holder | Fischione single-axis tomography holder |
| Tilt-axis relation | Parallel to the GST layer |
| Wafer, die, and device lineage | Not available |

## Tilt series

The intended acquisition contained 17 views from −40° to +40° at nominal 5° increments. One corrupted acquisition was discarded.

The 16 retained angles are:

```text
-40, -35, -30, -25, -20, -15, -10, -5,
  0, +10, +15, +20, +25, +30, +35, +40 degrees
```

The discarded acquisition is number `0010`, corresponding to nominal `+5°`.

Do not synthesize, duplicate, or interpolate the missing `+5°` projection in the archived data.

Public tilt-series arrays use:

```text
(A, V, U) = (16, 400, 300)
```

where `A` is tilt index, `V` is image row, and `U` is image column. `metadata/angles_deg.txt` is the authoritative angle coordinate.

## Raw EMD acquisitions

The current raw filenames use the normalized convention:

```text
D3_EDS-HAADF_0001_-40.emd
...
D3_EDS-HAADF_0017_+40.emd
```

The filename-to-angle mapping is recorded in `metadata/acquisition_manifest.csv`.

Each retained EMD contains:

### HAADF-STEM frame series

```text
shape: (400, 300, 50)
dtype: uint16
frames: 50
```

### EDS spectrum stream

```text
spectral bins: 4096
frames: 50
stream dtype: uint16
detector identifier: SuperXG1
```

An integrated spectrum of shape `(4096, 1)` and dtype `uint32` is also present.

### Embedded elemental maps

Velox-rendered float32 net-intensity maps are present for:

```text
N, O, Si, Ti, Ge, Sb, Te
```

The embedded map-processing settings include a 3 × 3 mean filter. These maps are processed analytical products, not raw event data or calibrated concentrations.

## Derived files

| File | Shape | Dtype | Interpretation |
|---|---:|---|---|
| `HAADF_stack.tif` | `(16, 400, 300)` | `uint16` | One extracted HAADF projection per retained tilt |
| `HAADF_aligned.tiff` | `(16, 400, 300)` | `float32` | HAADF tilt series aligned to the 0° acquisition |
| `Ge_stack.tif` | `(16, 400, 300)` | `float32` | Ge net-intensity tilt series |
| `Sb_stack.tif` | `(16, 400, 300)` | `float32` | Sb net-intensity tilt series |
| `Te_stack.tif` | `(16, 400, 300)` | `float32` | Te net-intensity tilt series |
| `Ti_stack.tif` | `(16, 400, 300)` | `float32` | Ti net-intensity tilt series |
| `Si_stack.tif` | `(16, 400, 300)` | `float32` | Si net-intensity tilt series |
| `ali_haadf.json` | 16 integer pairs | — | Pixel translations used to align each HAADF projection to the 0° acquisition |

The element-specific TIFF values are net intensities, not atomic concentrations.

## HAADF alignment file

`ali_haadf.json` contains one pair of integer pixel shifts for each projection, in stack order. Each pair specifies the translation used to align that acquisition to the 0° HAADF projection.

Conceptually:

```json
[
  [9, 2],
  ...
  [0, 0],
  ...
]
```

The `[0, 0]` entry corresponds to the 0° reference projection.

The following low-level convention remains undocumented:

- whether each pair is ordered as `[x, y]`, `[column, row]`, or `[row, column]`;
- whether values encode the applied shift or the measured displacement;
- interpolation and boundary handling used to produce `HAADF_aligned.tiff`.

The shift units are pixels.

## Elemental lines and later preprocessing

The associated publication reports net-count extraction using:

| Element | Emission line |
|---|---|
| Ge | Kα |
| Te | Lα |
| Sb | Lα |
| Ti | Kα |

The publication workflow reports:

1. translation-only alignment with Fiji MultiStackReg;
2. transform estimation from Ge maps;
3. application of the same transformations to Te, Sb, and Ti;
4. later crop/resampling to `176 × 112`;
5. binning factor 2;
6. independent maximum normalization per element before reconstruction.

The distributed `(16, 400, 300)` TIFF stacks correspond to an earlier stage than the final reconstruction inputs.

`ali_haadf.json` describes HAADF-to-0° alignment and should not automatically be equated with the separate Ge-derived elemental-map transformations.

## Repository organization

```text
.
├── README.md
├── LICENSE
├── CITATION.cff
│
├── metadata/
│   ├── dataset.yaml
│   ├── acquisition_manifest.csv
│   ├── angles_deg.txt
│   ├── processing.yaml
│   ├── checksums.sha256
│   └── audit/
│
├── raw/
│   └── emd/
│       ├── D3_EDS-HAADF_0001_-40.emd
│       ├── ...
│       └── D3_EDS-HAADF_0017_+40.emd
│
├── derived/
│   ├── haadf/
│   │   ├── HAADF_stack.tif
│   │   ├── HAADF_aligned.tiff
│   │   └── alignment/
│   │       └── ali_haadf.json
│   └── eds/
│       └── elemental_tilt_series/
│           ├── Ge_stack.tif
│           ├── Sb_stack.tif
│           ├── Te_stack.tif
│           ├── Ti_stack.tif
│           └── Si_stack.tif
│
├── previews/
└── scripts/
    └── audit_themis_dataset.py
```

## Loading the derived data

```python
from pathlib import Path

import json
import numpy as np
import tifffile

root = Path(".")

haadf = tifffile.imread(root / "derived/haadf/HAADF_aligned.tiff")
angles = np.loadtxt(root / "metadata/angles_deg.txt", dtype=np.float64)

with (root / "derived/haadf/alignment/ali_haadf.json").open() as handle:
    haadf_pixel_shifts = np.asarray(json.load(handle), dtype=np.int64)

assert haadf.shape == (16, 400, 300)
assert angles.shape == (16,)
assert haadf_pixel_shifts.shape == (16, 2)
```

## Intended uses

Potential uses include:

- limited-angle HAADF-STEM tomography;
- STEM-EDS chemical tomography;
- multichannel reconstruction;
- raw spectrum-stream reprocessing;
- frame-aware denoising and registration;
- irregular-angle reconstruction;
- joint HAADF/EDS methods;
- semiconductor-device characterization.

The dataset does not contain an independently validated ground-truth reconstruction.

## Known limitations

- The meaning of the internal lamella code `b2_d3` is undocumented.
- It remains unknown whether `b2_d3` is the virgin or SET device.
- The exact Titan Themis generation/submodel is undocumented.
- Wafer, die, and device lineage are unavailable.
- The exact 50-frame HAADF combination method is undocumented.
- The component order and sign convention in `ali_haadf.json` remain undocumented.
- N and O maps are retained inside the EMD files but not exported as public TIFF stacks.
- Net-intensity maps are not quantitative concentration maps.
- No independently validated 3D ground truth is included.

## Associated publication

This dataset is the experimental dataset associated with:

> Daniel del Pozo Bueno, Serge Brosset, Theo Monniez, Gabriele Navarro, Philippe Ciuciu, and Zineb Saghi.  
> **Unsupervised Deep Learning for Limited-Angle STEM-EDX Tomography — Application to 3D Chemical Analysis of Phase-Change Memory Devices.**  
> arXiv:2606.10547, 2026. DOI: `10.48550/arXiv.2606.10547`.

## Associated repository

This dataset is associated to the repository:

https://github.com/CEA-MetroCarac/DL_etomo

## License

This dataset is released under the **Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International** license:

```text
CC BY-NC-ND 4.0
```

You may share the unmodified dataset with attribution for non-commercial purposes. Distribution of adapted or modified versions is not permitted under this license. Consult the license text for the authoritative legal terms.

## Citation

Use the dataset citation in `CITATION.cff` and cite the associated publication when using these data in scientific work.

## Contacts

- **Dataset curator:** Daniele Picone — `daniele.picone@cea.fr`
- **Scientific contact:** Daniel Del Pozo Bueno — `daniel.delpozobueno@cea.fr`
- **PFNC contact:** Zineb Saghi — `zineb.saghi@cea.fr`
- **Original acquisition:** Zineb Saghi - `zineb.saghi@cea.fr`
- **Organization:** CEA-Leti, Grenoble