# anu_ctlab_qemscan_bse_to_zarr3
Convert QEMSCAN data to the Zarr V3 storage format with OME-Zarr metadata.
Supports `BSE` and `classification-results` image pyramids.
Unlike the export functionality available in `nanomin`, this method retains the original data type (e.g. 16-bit).
## Installation
```shell
pip install anu-ctlab-qemscan-bse-to-zarr3
```
## Usage (CLI)
```text
Usage: qemscan_bse_to_zarr3 [OPTIONS] INPUT OUTPUT
Convert QEMSCAN data to a Zarr V3 image pyramid with OME-Zarr metadata.
By default, outputs the BSE image. Specify a path in Data/classification-results to output that data.
╭─ Arguments ────────────────────────────────────────────────────────────────────╮
│ * input PATH Input QEMSCAN data directory [default: None] [required] │
│ * output PATH Input Zarr V3 directory [default: None] [required] │
╰────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ──────────────────────────────────────────────────────────────────────╮
│ --debug --no-debug Print debug information [default: no-debug] │
│ --help Show this message and exit. │
╰────────────────────────────────────────────────────────────────────────────────╯
```
This tool expects input structured as follows:
```text
SAMPLE_NAME
├── BSE from Nanomin.tif
├── Data
│ ├── BSE
│ ├── classification-results
│ ├── XRayData.db
│ ├── XRayData.isdx
│ └── XRayData.isdx.idx
└── SAMPLE_NAME.MapsMinData
```
If given the `SAMPLE_NAME` path, the tool will automatically convert the data in the `BSE` directory.
For example:
```bash
qemscan_bse_to_zarr3 SAMPLE_NAME output.zarr
```
This tool can also convert images in `classification-results` if the full path is specified.
For example:
```bash
qemscan_bse_to_zarr3 "SAMPLE_NAME/Data/classification-results/Element\ 8" output.zarr
```
Multi-channel image pyramids are not currently supported, such as those in `SAMPLE_NAME/Data/Merged Results`.
Raw data
{
"_id": null,
"home_page": null,
"name": "anu-ctlab-qemscan-bse-to-zarr3",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.12",
"maintainer_email": null,
"keywords": "bse, qemscan, zarr, zarr-v3",
"author": null,
"author_email": "Lachlan Deakin <ljdgit@gmail.com>",
"download_url": "https://files.pythonhosted.org/packages/12/da/57da0757372614bc903a49918dd1851d2eee2d8d14b469eb7a7c006cfc3b/anu_ctlab_qemscan_bse_to_zarr3-0.1.1.tar.gz",
"platform": null,
"description": "# anu_ctlab_qemscan_bse_to_zarr3\n\nConvert QEMSCAN data to the Zarr V3 storage format with OME-Zarr metadata.\nSupports `BSE` and `classification-results` image pyramids.\n\nUnlike the export functionality available in `nanomin`, this method retains the original data type (e.g. 16-bit).\n\n## Installation\n\n```shell\npip install anu-ctlab-qemscan-bse-to-zarr3\n```\n\n## Usage (CLI)\n\n```text\n Usage: qemscan_bse_to_zarr3 [OPTIONS] INPUT OUTPUT\n\n Convert QEMSCAN data to a Zarr V3 image pyramid with OME-Zarr metadata.\n By default, outputs the BSE image. Specify a path in Data/classification-results to output that data.\n\n\u256d\u2500 Arguments \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 * input PATH Input QEMSCAN data directory [default: None] [required] \u2502\n\u2502 * output PATH Input Zarr V3 directory [default: None] [required] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --debug --no-debug Print debug information [default: no-debug] \u2502\n\u2502 --help Show this message and exit. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\nThis tool expects input structured as follows:\n```text\nSAMPLE_NAME\n\u251c\u2500\u2500 BSE from Nanomin.tif\n\u251c\u2500\u2500 Data\n\u2502 \u251c\u2500\u2500 BSE\n\u2502 \u251c\u2500\u2500 classification-results\n\u2502 \u251c\u2500\u2500 XRayData.db\n\u2502 \u251c\u2500\u2500 XRayData.isdx\n\u2502 \u2514\u2500\u2500 XRayData.isdx.idx\n\u2514\u2500\u2500 SAMPLE_NAME.MapsMinData\n```\n\nIf given the `SAMPLE_NAME` path, the tool will automatically convert the data in the `BSE` directory.\nFor example:\n```bash\nqemscan_bse_to_zarr3 SAMPLE_NAME output.zarr\n```\n\nThis tool can also convert images in `classification-results` if the full path is specified.\nFor example:\n```bash\nqemscan_bse_to_zarr3 \"SAMPLE_NAME/Data/classification-results/Element\\ 8\" output.zarr\n```\n\nMulti-channel image pyramids are not currently supported, such as those in `SAMPLE_NAME/Data/Merged Results`.\n",
"bugtrack_url": null,
"license": "MIT License",
"summary": "Convert QEMSCAN data to a Zarr V3 image pyramid with OME-Zarr metadata",
"version": "0.1.1",
"project_urls": {
"Changelog": "https://github.com/MaterialsPhysicsANU/anu_ctlab_qemscan_bse_to_zarr3/blob/main/CHANGELOG.md",
"Repository": "https://github.com/MaterialsPhysicsANU/anu_ctlab_qemscan_bse_to_zarr3.git"
},
"split_keywords": [
"bse",
" qemscan",
" zarr",
" zarr-v3"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "fe47f5adc0125fb43781b15e590f9c1f192d21087d747046d9204643546fb6ca",
"md5": "385fa9085fa4c33e2edb16cb7e0d5102",
"sha256": "f6328cddb5e982e248c3a457add5466738e34a8c37009afd13be5c1764c00bef"
},
"downloads": -1,
"filename": "anu_ctlab_qemscan_bse_to_zarr3-0.1.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "385fa9085fa4c33e2edb16cb7e0d5102",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.12",
"size": 4704,
"upload_time": "2025-01-07T04:18:33",
"upload_time_iso_8601": "2025-01-07T04:18:33.749313Z",
"url": "https://files.pythonhosted.org/packages/fe/47/f5adc0125fb43781b15e590f9c1f192d21087d747046d9204643546fb6ca/anu_ctlab_qemscan_bse_to_zarr3-0.1.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "12da57da0757372614bc903a49918dd1851d2eee2d8d14b469eb7a7c006cfc3b",
"md5": "e1b33f4ac03dc1bf5d49c05b772a39a5",
"sha256": "91b902b5ac4ab9fa1f5f888a375770ea588f37b7e9350e6ebf630698d99f7d38"
},
"downloads": -1,
"filename": "anu_ctlab_qemscan_bse_to_zarr3-0.1.1.tar.gz",
"has_sig": false,
"md5_digest": "e1b33f4ac03dc1bf5d49c05b772a39a5",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.12",
"size": 28607,
"upload_time": "2025-01-07T04:18:36",
"upload_time_iso_8601": "2025-01-07T04:18:36.489826Z",
"url": "https://files.pythonhosted.org/packages/12/da/57da0757372614bc903a49918dd1851d2eee2d8d14b469eb7a7c006cfc3b/anu_ctlab_qemscan_bse_to_zarr3-0.1.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2025-01-07 04:18:36",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "MaterialsPhysicsANU",
"github_project": "anu_ctlab_qemscan_bse_to_zarr3",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "anu-ctlab-qemscan-bse-to-zarr3"
}
JSON
