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Add Grapevine Petiole Dehydration datasets #57

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106 changes: 60 additions & 46 deletions docs/source/data/docs.data.petioles.rst
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Expand Up @@ -32,7 +32,7 @@ The datasets were acquired at the Advanced Light Source (ALS) beamline 8.3.2 in

The dataset includes 14 raw tomographic scans divided into two dynamic dehydration sequences, along with a unified archive of high-quality expert-curated segmentation masks:

* **Expert-curated Masks**: :download:`annotations.tar.zst <https://zenodo.org/records/19476729/files/annotations.tar.zst>` - Semantic instances for 42 cross-sections (background, cortex, phloem fibers, phloem, hydrated xylem, air-filled pith, water-filled pith, dehydrated xylem, and ignore regions).
* **Expert-curated Masks**: :download:`annotations.tar.zst <https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fannotations.tar.zst>` - Semantic instances for 42 cross-sections (background, cortex, phloem fibers, phloem, hydrated xylem, air-filled pith, water-filled pith, dehydrated xylem, and ignore regions).
* **Time Series 1**: 6 sequential scans of a single grapevine petiole undergoing dehydration (Petioles 22-27).
* **Time Series 2**: 8 sequential scans of a second grapevine petiole undergoing dehydration (Petioles 33-40).

Expand All @@ -44,49 +44,63 @@ To load the datasets and perform a basic reconstruction using `tomopy <https://t
:width: 20pt
:height: 20pt

+-----------------------+----------+-------------------------------------------------+----------------+
| Tomo ID | Sequence | Sample / Filename | Image Preview |
+=======================+==========+=================================================+================+
| petiole_22_ | TS1 | 20260221_135217_petiole22.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_23_ | TS1 | 20260221_140347_petiole23.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_24_ | TS1 | 20260221_140816_petiole24.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_25_ | TS1 | 20260221_141434_petiole25.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_26_ | TS1 | 20260221_141945_petiole26.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_27_ | TS1 | 20260221_142453_petiole27.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_33_ | TS2 | 20260221_154210_petiole33.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_34_ | TS2 | 20260221_154714_petiole34.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_35_ | TS2 | 20260221_155149_petiole35.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_36_ | TS2 | 20260221_155821_petiole36.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_37_ | TS2 | 20260221_160336_petiole37.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_38_ | TS2 | 20260221_160807_petiole38.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_39_ | TS2 | 20260221_161542_petiole39.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
| petiole_40_ | TS2 | 20260221_162040_petiole40.h5 | |grapevine| |
+-----------------------+----------+-------------------------------------------------+----------------+
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| Tomo ID | Sequence | Sample / Filename | Image Preview | Reconstruction |
+=======================+==========+=================================================+================+==================+
| petiole_22_ | TS1 | 20260221_135217_petiole22.h5 | |grapevine| | rec_22_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_23_ | TS1 | 20260221_140347_petiole23.h5 | |grapevine| | rec_23_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_24_ | TS1 | 20260221_140816_petiole24.h5 | |grapevine| | rec_24_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_25_ | TS1 | 20260221_141434_petiole25.h5 | |grapevine| | rec_25_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_26_ | TS1 | 20260221_141945_petiole26.h5 | |grapevine| | rec_26_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_27_ | TS1 | 20260221_142453_petiole27.h5 | |grapevine| | rec_27_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_33_ | TS2 | 20260221_154210_petiole33.h5 | |grapevine| | rec_33_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_34_ | TS2 | 20260221_154714_petiole34.h5 | |grapevine| | rec_34_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_35_ | TS2 | 20260221_155149_petiole35.h5 | |grapevine| | rec_35_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_36_ | TS2 | 20260221_155821_petiole36.h5 | |grapevine| | rec_36_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_37_ | TS2 | 20260221_160336_petiole37.h5 | |grapevine| | rec_37_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_38_ | TS2 | 20260221_160807_petiole38.h5 | |grapevine| | rec_38_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_39_ | TS2 | 20260221_161542_petiole39.h5 | |grapevine| | rec_39_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+
| petiole_40_ | TS2 | 20260221_162040_petiole40.h5 | |grapevine| | rec_40_ |
+-----------------------+----------+-------------------------------------------------+----------------+------------------+

.. _petiole_22: https://zenodo.org/records/19476729/files/petiole22_raw_rec.tar.zst
.. _petiole_23: https://zenodo.org/records/19476729/files/petiole23_raw_rec.tar.zst
.. _petiole_24: https://zenodo.org/records/19476729/files/petiole24_raw_rec.tar.zst
.. _petiole_25: https://zenodo.org/records/19476729/files/petiole25_raw_rec.tar.zst
.. _petiole_26: https://zenodo.org/records/19476729/files/petiole26_raw_rec.tar.zst
.. _petiole_27: https://zenodo.org/records/19476729/files/petiole27_raw_rec.tar.zst
.. _petiole_33: https://zenodo.org/records/19476729/files/petiole33_raw_rec.tar.zst
.. _petiole_34: https://zenodo.org/records/19476729/files/petiole34_raw_rec.tar.zst
.. _petiole_35: https://zenodo.org/records/19476729/files/petiole35_raw_rec.tar.zst
.. _petiole_36: https://zenodo.org/records/19476729/files/petiole36_raw_rec.tar.zst
.. _petiole_37: https://zenodo.org/records/19476729/files/petiole37_raw_rec.tar.zst
.. _petiole_38: https://zenodo.org/records/19476729/files/petiole38_raw_rec.tar.zst
.. _petiole_39: https://zenodo.org/records/19476729/files/petiole39_raw_rec.tar.zst
.. _petiole_40: https://zenodo.org/records/19476729/files/petiole40_raw_rec.tar.zst
.. _petiole_22: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_135217_petiole22.h5
.. _petiole_23: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_140347_petiole23.h5
.. _petiole_24: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_140816_petiole24.h5
.. _petiole_25: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_141434_petiole25.h5
.. _petiole_26: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_141945_petiole26.h5
.. _petiole_27: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_142453_petiole27.h5
.. _petiole_33: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_154210_petiole33.h5
.. _petiole_34: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_154714_petiole34.h5
.. _petiole_35: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_155149_petiole35.h5
.. _petiole_36: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_155821_petiole36.h5
.. _petiole_37: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_160336_petiole37.h5
.. _petiole_38: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_160807_petiole38.h5
.. _petiole_39: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_161542_petiole39.h5
.. _petiole_40: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Fraw%2F20260221_162040_petiole40.h5
.. _rec_22: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole22%2F
.. _rec_23: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole23%2F
.. _rec_24: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole24%2F
.. _rec_25: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole25%2F
.. _rec_26: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole26%2F
.. _rec_27: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole27%2F
.. _rec_33: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole33%2F
.. _rec_34: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole34%2F
.. _rec_35: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole35%2F
.. _rec_36: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole36%2F
.. _rec_37: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole37%2F
.. _rec_38: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole38%2F
.. _rec_39: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole39%2F
.. _rec_40: https://app.globus.org/file-manager?destination_id=472d6c6f-dc53-420f-9a12-b3515282f1c1&destination_path=%2Ftomobank_petioles%2Freconstruction%2Fpetiole40%2F