initial yeast + motorbench

.gitignore

@@ -1 +1,2 @@
-scripts/
+scripts/
+.idea/

README.md

@@ -1,5 +1,5 @@
 ---
-license: cc-by-4.0
+license: cc0-1.0
 language:
 - en
 pretty_name: POPSICLE
@@ -23,6 +23,8 @@ configs:
   data_files: phantom/Croissant/runs.csv
 - config_name: bacterial
   data_files: bacterial/Croissant/runs.csv
+- config_name: yeast
+  data_files: yeast/Croissant/runs.csv
 ---
 
 # Dataset Card for POPSICLE
@@ -54,27 +56,28 @@ protocol) so models can be trained and compared under one roof.
 | Sub-benchmark | Task          | Organism / sample        | # train | # test | Status      |
 |---------------|---------------|--------------------------|--------:|-------:|-------------|
 | **Phantom**   | Localization  | Lysate / synthetic        |       7 |    485 | ✅ released |
-| Yeast         | Segmentation  | *S. pombe*                |      15 |      4 | 🚧 pending  |
+| **Yeast**     | Segmentation  | *S. pombe*                |      16 |      4 | ✅ released |
 | **Bacterial** | Segmentation  | Prokaryote (8 genera)     |      68 |     12 | ✅ released |
 | MotorBench    | Localization  | *V. cholerae*             |   1,288 |    844 | 🚧 pending  |
 
 - **Curated by:** Authors of the POPSICLE benchmark paper (NeurIPS 2026, under review).
-- **Shared by:** Chan Zuckerberg Imaging Institute (CZII) / CryoET Data Portal community.
-- **License:** CC-BY-4.0 for the manifests + CSVs in this repo. The
-  underlying tomograms and annotations remain under their original CryoET
-  Data Portal terms (refer to each linked deposition for authoritative
-  licensing).
+- **Shared by:** Biohub Dynamic Structural Biology / CryoET Data Portal community.
+- **License:** **CC0-1.0** (Public Domain Dedication) — covers both the
+  manifests + CSVs in this repo and the underlying tomograms and
+  annotations on the CryoET Data Portal depositions linked above. No
+  attribution requirement; we still appreciate citation of the POPSICLE
+  paper and the benchmark publication.
 
 ### Dataset Sources
 
 - **Repository:** https://huggingface.co/datasets/uermel/popsicle
-- **Paper:** POPSICLE (anonymous, NeurIPS 2026 submission).
+- **Paper:** POPSICLE (NeurIPS 2026 submission).
 - **Underlying datasets:**
   [DS-10440](https://cryoetdataportal.czscience.com/datasets/10440) (Phantom train),
   [DS-10445](https://cryoetdataportal.czscience.com/datasets/10445) (Phantom public test),
   [DS-10446](https://cryoetdataportal.czscience.com/datasets/10446) (Phantom private test),
   [CZCDP-10350](https://cryoetdataportal.czscience.com/depositions/10350) (Bacterial),
-  [DS-10000](https://cryoetdataportal.czscience.com/datasets/10000)/[DS-10001](https://cryoetdataportal.czscience.com/datasets/10001) (Yeast),
+  [CZCDP-10351](https://cryoetdataportal.czscience.com/depositions/10351) (Yeast; underlying tomograms in DS-10000/DS-10001),
   [CZCDP-10332](https://cryoetdataportal.czscience.com/depositions/10332)/[CZCDP-10347](https://cryoetdataportal.czscience.com/depositions/10347) (MotorBench train/test).
 - **Data Portal:** https://cryoetdataportal.czscience.com (Ermel et al.,
   *Nature Methods* 21:2200–2202, 2024).
@@ -124,7 +127,7 @@ popsicle/
       segmentations.csv
       objects.csv          # name, url
   bacterial/    # ✅ released — segmentation across 8 bacterial genera
-  yeast/        # 🚧 pending
+  yeast/        # ✅ released — segmentation in *S. pombe*
   motorbench/   # 🚧 pending
 ```
 
@@ -158,8 +161,7 @@ methods that generalize across particle scale and morphology.
 | `val`   | DS-10445    | 121         | CZII Kaggle "public test" set   |
 | `test`  | DS-10446    | 364         | CZII Kaggle "private test" set  |
 
-Picks are **restricted to the original ground-truth annotations**
-(author: Ariana Peck). Community-derived submissions hosted on the same
+Picks are **restricted to the original ground-truth annotations**. Community-derived submissions hosted on the same
 CDP datasets — including Kaggle challenge entries — are intentionally
 excluded so the benchmark scores against the canonical reference labels.
 
@@ -239,6 +241,69 @@ for seg in run.segmentations:
     print(seg.name, seg.voxel_size)
 ```
 
+### Yeast — multi-class organelle segmentation
+
+Dense voxel-wise segmentation of organelles in cryoET tomograms of
+*Schizosaccharomyces pombe* (fission yeast) — a low-data, high-variance
+eukaryotic counterpart to the well-sampled bacterial setting. 20
+tomograms from the two CryoET Data Portal *S. pombe* datasets
+([DS-10000](https://cryoetdataportal.czscience.com/datasets/10000),
+[DS-10001](https://cryoetdataportal.czscience.com/datasets/10001)),
+annotated with up to six organelle classes per run. Annotations are
+sourced from the POPSICLE Yeast Segmentation Dataset deposition
+([CZCDP-10351](https://cryoetdataportal.czscience.com/depositions/10351)).
+
+| Class                | Portal `object_name`        |
+|----------------------|-----------------------------|
+| `cytoplasm`          | `cytoplasm`                 |
+| `nucleus`            | `nucleus`                   |
+| `nuclear-envelope`   | `nuclear envelope`          |
+| `vesicle`            | `vesicle`                   |
+| `endomembrane`       | `membrane-enclosed lumen`   |
+| `mitochondrion`      | `mitochondrion`             |
+
+#### Splits
+
+| Split   | # tomograms | Notes                             |
+|---------|------------:|-----------------------------------|
+| `train` | 16          | All 16 from the user-supplied list|
+| `test`  | 4           | Held out from training            |
+
+Class distribution is uneven — large structures like `cytoplasm` are
+present in nearly every run, while small organelles (`vesicle`,
+`endomembrane`) are sparse and `mitochondrion` / `nucleus` are present
+in only a subset:
+
+| Class               | Total runs |
+|---------------------|-----------:|
+| `cytoplasm`         | 19         |
+| `endomembrane`      | 18         |
+| `vesicle`           | 18         |
+| `mitochondrion`     |  9         |
+| `nuclear-envelope`  |  8         |
+| `nucleus`           |  8         |
+
+This unevenness — together with the small total tomogram count — makes
+yeast a challenging low-data, class-imbalanced regime, complementary to
+the better-sampled bacterial benchmark (paper §4, §6, Table 2).
+
+#### Loading with copick
+
+```python
+import copick
+
+root = copick.from_croissant(
+    "https://huggingface.co/datasets/uermel/popsicle/resolve/main/yeast/Croissant/metadata.json",
+    static_fs_args={"anon": True},   # public portal bucket
+)
+
+print(root.splits)                   # {'train': [16 names], 'test': [4 names]}
+
+run = root.get_runs_in_split("train")[0]
+for seg in run.segmentations:
+    print(seg.name, seg.voxel_size)
+```
+
 ## Dataset Creation
 
 ### Curation Rationale
@@ -266,8 +331,8 @@ annotations become available rather than being a static challenge release
 #### Data Collection and Processing
 
 All source tomograms were acquired by tilt-series cryoET on vitrified
-biological samples and reconstructed via standard physics-based pipelines
-hosted on the CryoET Data Portal (paper §C). The portal uses
+biological samples and reconstructed via standard pipelines
+described on the CryoET Data Portal (paper §C). Biohub DSB uses
 [AreTomo3](https://doi.org/10.1101/2025.03.11.642690) for motion
 correction, tilt-series alignment, CTF correction, and weighted
 back-projection, with optional self-supervised denoising via DenoisET.
@@ -276,28 +341,55 @@ pipeline and ingested into the portal as DS-10440/10445/10446.
 
 #### Who are the source data producers?
 
-Source tomograms and reference annotations are produced by the
-contributing labs listed on each portal deposition. POPSICLE itself does
-not generate new acquisitions or annotations — it provides a unified
-manifest layer over published portal data.
+Provenance differs per sub-benchmark and is summarized below. Authoritative
+credits live on each portal deposition page linked under
+[Dataset Sources](#dataset-sources).
+
+| Sub-benchmark | Tomogram source                                     | Annotation source                                  |
+|---------------|-----------------------------------------------------|----------------------------------------------------|
+| **Phantom**   | Acquired and reconstructed by Biohub DSB.            | Created by Biohub DSB (Peck et al. 2025).          |
+| **Bacterial** | Contributed by external labs (8 bacterial genera).  | **Created by the POPSICLE authors.**               |
+| **Yeast**     | Acquired by external labs (de Teresa-Trueba et al.).| Curated/refined by Biohub DSB from prior releases. |
+| **MotorBench**| Contributed by external labs (BYU + collaborators). | Contributed by the BYU Kaggle community . |
+
+In short: POPSICLE produces some new annotations (Bacterial), curates
+others (Yeast), and indexes the rest (Phantom, MotorBench) — none of
+the underlying tomograms are re-acquired by this project.
 
 ### Annotations
 
 #### Annotation process
 
-For Phantom, a sample of recombinantly expressed and purified
-macromolecules was prepared in lysate-like conditions and imaged by
-cryoET; expert annotators identified the 3D centers of all six target
-classes per tomogram (Peck et al. 2025). Reference annotations are stored
-on the CryoET Data Portal as point picks under the original authors'
-identifiers.
+- **Phantom**: a sample of recombinantly expressed and purified
+  macromolecules was prepared in lysate-like conditions and imaged by
+  cryoET; Biohub DSB annotators identified the 3D centers of all six
+  target classes per tomogram (Peck et al. 2025). Annotations are stored
+  on the portal as point picks.
+- **Bacterial**: POPSICLE authors generated dense voxel-wise
+  segmentations across five compartment classes (cytosole, flagellum,
+  inclusion, intermembrane-space, membrane) on 80 cellular tomograms
+  from 8 bacterial genera, deposited as
+  [CZCDP-10350](https://cryoetdataportal.czscience.com/depositions/10350).
+- **Yeast** *(pending)*: organelle segmentations originally produced by
+  de Teresa-Trueba et al. 2023; curated and standardized by Biohub DSB
+  for inclusion in POPSICLE.
+- **MotorBench** *(pending)*: bacterial flagellar motor centers picked
+  by the BYU Kaggle competition contributors (training corpus expanded
+  by the first-place team and MIC-DKFZ); the held-out test set was
+  authored by Owens et al. 2025.
 
 #### Who are the annotators?
 
-Phantom ground-truth picks are credited to **Ariana Peck** on the CryoET
-Data Portal (and co-authors of Peck et al. 2025). Other sub-benchmarks
-inherit their respective expert authorship; see each portal deposition
-for the full credits.
+- **Phantom**: Ariana Peck and Biohub DSB co-authors of Peck et al.
+  2025 (point picks restricted to author "Ariana Peck" in this release
+  to exclude community Kaggle submissions hosted on the same datasets).
+- **Bacterial**: POPSICLE author team (CZCDP-10350 contributors —
+  Peck, Ermel, Schwartz, Owens, Carragher, Kimanius, and others).
+- **Yeast** *(pending)*: de Teresa-Trueba et al. 2023, with curatorial
+  refinement by Biohub DSB.
+- **MotorBench** *(pending)*: BYU competition + first-place team
+  (Brenden Artley) + MIC-DKFZ (Fabian Isensee et al.) for the training
+  corpus; Owens et al. 2025 (V. cholerae) for the held-out test set.
 
 #### Personal and Sensitive Information
 

bacterial/Croissant/metadata.json

@@ -57,7 +57,7 @@
   "description": "Multi-class compartment segmentation benchmark for bacterial cryo-electron tomograms, from the POPSICLE suite. 80 tomograms across 8 bacterial species (bdellovibrio, coxiella, hylemonella, hyphomonas, legionella, pseudomonas, salmonella, vibrio), split 68/12 train/test. Five segmentation classes: cytosole, flagellum, inclusion, intermembrane-space, membrane. Annotations sourced from CryoET Data Portal deposition CZCDP-10350 (POPSICLE Bacterial Segmentation Dataset).",
   "conformsTo": "http://mlcommons.org/croissant/1.1",
   "version": "1.23.4",
-  "license": "CC-BY-4.0",
+  "license": "CC0-1.0",
   "citeAs": "POPSICLE: Benchmark Datasets for Segmentation and Localization in CryoET (NeurIPS 2026, under review). Bacterial annotations: CryoET Data Portal deposition CZCDP-10350.",
   "datePublished": "2026-05-05",
   "copick:baseUrl": "s3://cryoet-data-portal-public/",

phantom/Croissant/metadata.json

@@ -57,7 +57,7 @@
   "description": "Multi-class macromolecular localization benchmark from the POPSICLE suite. Aggregates the three CryoET Data Portal Phantom datasets (DS-10440 train, DS-10445 public test, DS-10446 private test) into a single Croissant manifest with train/val/test splits. Six particle classes spanning ~270-4300 kDa. Picks are restricted to original ground-truth annotations (Peck et al. 2025), excluding community Kaggle submissions hosted on the same datasets. https://doi.org/10.1038/s41592-025-02800-5.",
   "conformsTo": "http://mlcommons.org/croissant/1.1",
   "version": "1.23.4",
-  "license": "CC-BY-4.0",
+  "license": "CC0-1.0",
   "citeAs": "Peck A et al. (2025). A realistic phantom dataset for benchmarking cryo-ET data annotation. Nature Methods 22:1819-1823. doi:10.1038/s41592-025-02800-5",
   "datePublished": "2026-05-05",
   "copick:baseUrl": "s3://cryoet-data-portal-public/",

yeast/Croissant/features.csv

@@ -0,0 +1 @@
+run,voxel_size,tomo_type,feature_type,url

yeast/Croissant/meshes.csv

@@ -0,0 +1 @@
+run,user_id,session_id,object_name,url,sha256

yeast/Croissant/metadata.json

@@ -0,0 +1,1075 @@
+{
+  "@context": {
+    "@language": "en",
+    "@vocab": "https://schema.org/",
+    "citeAs": "cr:citeAs",
+    "column": "cr:column",
+    "conformsTo": "dct:conformsTo",
+    "containedIn": "cr:containedIn",
+    "copick": "https://copick.org/schema/",
+    "copick:baseUrl": "copick:baseUrl",
+    "copick:config": {
+      "@id": "copick:config",
+      "@type": "@json"
+    },
+    "cr": "http://mlcommons.org/croissant/",
+    "rai": "http://mlcommons.org/croissant/RAI/",
+    "data": {
+      "@id": "cr:data",
+      "@type": "@json"
+    },
+    "dataType": {
+      "@id": "cr:dataType",
+      "@type": "@vocab"
+    },
+    "dct": "http://purl.org/dc/terms/",
+    "examples": {
+      "@id": "cr:examples",
+      "@type": "@json"
+    },
+    "extract": "cr:extract",
+    "field": "cr:field",
+    "fileProperty": "cr:fileProperty",
+    "fileObject": "cr:fileObject",
+    "fileSet": "cr:fileSet",
+    "format": "cr:format",
+    "includes": "cr:includes",
+    "isLiveDataset": "cr:isLiveDataset",
+    "jsonPath": "cr:jsonPath",
+    "key": "cr:key",
+    "md5": "cr:md5",
+    "parentField": "cr:parentField",
+    "path": "cr:path",
+    "recordSet": "cr:recordSet",
+    "references": "cr:references",
+    "regex": "cr:regex",
+    "repeated": "cr:repeated",
+    "replace": "cr:replace",
+    "samplingRate": "cr:samplingRate",
+    "sc": "https://schema.org/",
+    "separator": "cr:separator",
+    "source": "cr:source",
+    "subField": "cr:subField",
+    "transform": "cr:transform"
+  },
+  "@type": "sc:Dataset",
+  "name": "POPSICLE Yeast Segmentation",
+  "description": "Multi-class organelle segmentation benchmark for Schizosaccharomyces pombe (fission yeast) cryo-electron tomograms, from the POPSICLE suite. 20 tomograms drawn from CryoET Data Portal datasets DS-10000 and DS-10001, split 16/4 train/test. Six segmentation classes: cytoplasm, nucleus, nuclear-envelope, vesicle, endomembrane, mitochondrion. Annotations sourced from deposition CZCDP-10351 (POPSICLE Yeast Segmentation Dataset).",
+  "conformsTo": "http://mlcommons.org/croissant/1.1",
+  "version": "1.23.4",
+  "license": "CC0-1.0",
+  "citeAs": "POPSICLE: Benchmark Datasets for Segmentation and Localization in CryoET (NeurIPS 2026, under review). Yeast annotations: CryoET Data Portal deposition CZCDP-10351.",
+  "datePublished": "2026-05-05",
+  "copick:baseUrl": "s3://cryoet-data-portal-public/",
+  "copick:config": {
+    "name": "CZ cryoET Data Portal Dataset",
+    "description": "This copick project contains data from datasets [10000, 10001].",
+    "version": "1.23.4",
+    "user_id": null,
+    "session_id": null,
+    "pickable_objects": [
+      {
+        "name": "golgi-apparatus",
+        "is_particle": false,
+        "label": 1,
+        "color": [
+          0,
+          255,
+          0,
+          255
+        ],
+        "emdb_id": "EMD-14412",
+        "pdb_id": null,
+        "identifier": "GO:0005794",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "vesicle",
+        "is_particle": false,
+        "label": 2,
+        "color": [
+          255,
+          0,
+          255,
+          255
+        ],
+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0031982",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "nuclear-envelope",
+        "is_particle": false,
+        "label": 3,
+        "color": [
+          0,
+          127,
+          255,
+          255
+        ],
+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0005635",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "nucleus",
+        "is_particle": false,
+        "label": 4,
+        "color": [
+          255,
+          127,
+          0,
+          255
+        ],
+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0005634",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "endoplasmic-reticulum",
+        "is_particle": false,
+        "label": 5,
+        "color": [
+          127,
+          191,
+          127,
+          255
+        ],
+        "emdb_id": "EMD-14412",
+        "pdb_id": null,
+        "identifier": "GO:0005783",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "lipid-droplet",
+        "is_particle": false,
+        "label": 6,
+        "color": [
+          94,
+          6,
+          164,
+          255
+        ],
+        "emdb_id": "EMD-14412",
+        "pdb_id": null,
+        "identifier": "GO:0005811",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "mitochondrion",
+        "is_particle": false,
+        "label": 7,
+        "color": [
+          233,
+          1,
+          56,
+          255
+        ],
+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0005739",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "vacuole",
+        "is_particle": false,
+        "label": 8,
+        "color": [
+          211,
+          254,
+          9,
+          255
+        ],
+        "emdb_id": "EMD-14412",
+        "pdb_id": null,
+        "identifier": "GO:0005773",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "multivesicular-body",
+        "is_particle": false,
+        "label": 9,
+        "color": [
+          0,
+          255,
+          255,
+          255
+        ],
+        "emdb_id": "EMD-14412",
+        "pdb_id": null,
+        "identifier": "GO:0005771",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "fatty-acid-synthase-complex",
+        "is_particle": true,
+        "label": 10,
+        "color": [
+          193,
+          119,
+          247,
+          255
+        ],
+        "emdb_id": "EMD-14412",
+        "pdb_id": null,
+        "identifier": "GO:0005835",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "membrane",
+        "is_particle": false,
+        "label": 11,
+        "color": [
+          3,
+          112,
+          74,
+          255
+        ],
+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0016020",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "endomembrane",
+        "is_particle": false,
+        "label": 12,
+        "color": [
+          128,
+          66,
+          8,
+          255
+        ],
+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0031974",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {
+          "portal_original_name": "membrane-enclosed-lumen"
+        }
+      },
+      {
+        "name": "microtubule",
+        "is_particle": false,
+        "label": 13,
+        "color": [
+          0,
+          255,
+          127,
+          255
+        ],
+        "emdb_id": "EMD-14412",
+        "pdb_id": null,
+        "identifier": "GO:0005874",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "cytosolic-ribosome",
+        "is_particle": true,
+        "label": 14,
+        "color": [
+          0,
+          0,
+          255,
+          255
+        ],
+        "emdb_id": "EMD-14412",
+        "pdb_id": null,
+        "identifier": "GO:0022626",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "cytoplasm",
+        "is_particle": false,
+        "label": 15,
+        "color": [
+          250,
+          187,
+          117,
+          255
+        ],
+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0005737",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      }
+    ]
+  },
+  "distribution": [
+    {
+      "@type": "cr:FileObject",
+      "@id": "runs-csv",
+      "name": "runs-csv",
+      "contentUrl": "https://huggingface.co/datasets/uermel/popsicle/resolve/main/yeast/Croissant/runs.csv",
+      "encodingFormat": "text/csv",
+      "sha256": "23a770615566b4028652dfe47b00e818c6cb324576ed4cedcc461c5da763882a"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "voxel-spacings-csv",
+      "name": "voxel-spacings-csv",
+      "contentUrl": "https://huggingface.co/datasets/uermel/popsicle/resolve/main/yeast/Croissant/voxel_spacings.csv",
+      "encodingFormat": "text/csv",
+      "sha256": "f9075077c6a80d3df684ab0785c8bd1bdf69fd25c40b1b4c207fa3bd0e86147b"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "tomograms-csv",
+      "name": "tomograms-csv",
+      "contentUrl": "https://huggingface.co/datasets/uermel/popsicle/resolve/main/yeast/Croissant/tomograms.csv",
+      "encodingFormat": "text/csv",
+      "sha256": "44a330872b4bbfd5a6ef3ca43025cfdcbac58cf320d8c37d8cc5633db1d54e1a"
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+          "@id": "copick/features/feature_type",
+          "dataType": "sc:Text",
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+          "@id": "copick/features/url",
+          "dataType": "sc:Text",
+          "source": {
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+            "extract": {
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+      "@id": "copick/picks",
+      "name": "picks",
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+          "@id": "copick/picks/run",
+          "dataType": "sc:Text",
+          "source": {
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+            },
+            "extract": {
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+        },
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+          "@id": "copick/picks/user_id",
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+          }
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+          "@id": "copick/picks/session_id",
+          "dataType": "sc:Text",
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+            },
+            "extract": {
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+            }
+          }
+        },
+        {
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+          "dataType": "sc:Text",
+          "source": {
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+            "extract": {
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+          }
+        },
+        {
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+          "@id": "copick/picks/url",
+          "dataType": "sc:Text",
+          "source": {
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+          "@id": "copick/picks/sha256",
+          "dataType": "sc:Text",
+          "source": {
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+            },
+            "extract": {
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+          }
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+          "@type": "cr:Field",
+          "@id": "copick/picks/portal_object_name",
+          "dataType": "sc:Text",
+          "source": {
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+            },
+            "extract": {
+              "column": "portal_object_name"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/picks/portal_session_id",
+          "dataType": "sc:Text",
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+            }
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+          "dataType": "sc:Text",
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+            },
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+        {
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+          "@id": "copick/picks/portal_annotation_file_id",
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+          "dataType": "sc:Text",
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+            },
+            "extract": {
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+          "@id": "copick/meshes/url",
+          "dataType": "sc:Text",
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+            },
+            "extract": {
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+            }
+          }
+        },
+        {
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+          "@id": "copick/meshes/sha256",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
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+            },
+            "extract": {
+              "column": "sha256"
+            }
+          }
+        }
+      ]
+    },
+    {
+      "@type": "cr:RecordSet",
+      "@id": "copick/segmentations",
+      "name": "segmentations",
+      "field": [
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+          "@id": "copick/segmentations/run",
+          "dataType": "sc:Text",
+          "source": {
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+            },
+            "extract": {
+              "column": "run"
+            }
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+        {
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+          "@id": "copick/segmentations/voxel_size",
+          "dataType": "sc:Float",
+          "source": {
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+            },
+            "extract": {
+              "column": "voxel_size"
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+          }
+        },
+        {
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+          "@id": "copick/segmentations/user_id",
+          "dataType": "sc:Text",
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+            },
+            "extract": {
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+          "dataType": "sc:Text",
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+            },
+            "extract": {
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+        {
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+          "dataType": "sc:Text",
+          "source": {
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+            },
+            "extract": {
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+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/segmentations/is_multilabel",
+          "dataType": "sc:Boolean",
+          "source": {
+            "fileObject": {
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+            },
+            "extract": {
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+            }
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+        {
+          "@type": "cr:Field",
+          "@id": "copick/segmentations/url",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
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+            },
+            "extract": {
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+            }
+          }
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+        {
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+          "@id": "copick/segmentations/portal_object_name",
+          "dataType": "sc:Text",
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+            },
+            "extract": {
+              "column": "portal_object_name"
+            }
+          }
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+        {
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+          "dataType": "sc:Text",
+          "source": {
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+            },
+            "extract": {
+              "column": "portal_session_id"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/segmentations/portal_annotation_id",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "segmentations-csv"
+            },
+            "extract": {
+              "column": "portal_annotation_id"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/segmentations/portal_annotation_file_id",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "segmentations-csv"
+            },
+            "extract": {
+              "column": "portal_annotation_file_id"
+            }
+          }
+        }
+      ]
+    },
+    {
+      "@type": "cr:RecordSet",
+      "@id": "copick/objects",
+      "name": "objects",
+      "field": [
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+          "@type": "cr:Field",
+          "@id": "copick/objects/name",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "objects-csv"
+            },
+            "extract": {
+              "column": "name"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/objects/url",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "objects-csv"
+            },
+            "extract": {
+              "column": "url"
+            }
+          }
+        }
+      ]
+    },
+    {
+      "@type": "cr:RecordSet",
+      "@id": "copick/splits",
+      "name": "splits",
+      "description": "Maps split names to MLCommons definition URLs.",
+      "key": {
+        "@id": "copick/splits/name"
+      },
+      "field": [
+        {
+          "@type": "cr:Field",
+          "@id": "copick/splits/name",
+          "dataType": "sc:Text"
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/splits/url",
+          "dataType": "sc:URL"
+        }
+      ],
+      "data": [
+        {
+          "copick/splits/name": "train",
+          "copick/splits/url": "https://mlcommons.org/definitions/training_split"
+        },
+        {
+          "copick/splits/name": "test",
+          "copick/splits/url": "https://mlcommons.org/definitions/test_split"
+        }
+      ]
+    }
+  ]
+}

yeast/Croissant/objects.csv

@@ -0,0 +1 @@
+name,url

yeast/Croissant/picks.csv

@@ -0,0 +1 @@
+run,user_id,session_id,object_name,url,sha256,portal_object_name,portal_session_id,portal_annotation_id,portal_annotation_file_id

yeast/Croissant/runs.csv

@@ -0,0 +1,21 @@
+name,portal_run_id,split
+249,249,train
+241,241,train
+242,242,train
+243,243,train
+244,244,train
+245,245,train
+246,246,train
+247,247,test
+248,248,test
+250,250,test
+253,253,train
+252,252,train
+254,254,train
+255,255,train
+256,256,train
+257,257,train
+258,258,train
+259,259,train
+260,260,train
+251,251,test

yeast/Croissant/segmentations.csv

@@ -0,0 +1,81 @@
+run,voxel_size,user_id,session_id,name,is_multilabel,url,portal_object_name,portal_session_id,portal_annotation_id,portal_annotation_file_id
+249,13.48,data-portal,246334,nuclear-envelope,false,10000/TS_043/Reconstructions/VoxelSpacing13.480/Annotations/116/nuclear_envelope-1.0_segmentationmask.zarr,nuclear envelope,,134609,246334
+249,13.48,data-portal,246338,endomembrane,false,10000/TS_043/Reconstructions/VoxelSpacing13.480/Annotations/118/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134611,246338
+249,13.48,data-portal,246336,vesicle,false,10000/TS_043/Reconstructions/VoxelSpacing13.480/Annotations/117/vesicle-1.0_segmentationmask.zarr,vesicle,,134610,246336
+249,13.48,data-portal,246330,cytoplasm,false,10000/TS_043/Reconstructions/VoxelSpacing13.480/Annotations/114/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134607,246330
+249,13.48,data-portal,246332,nucleus,false,10000/TS_043/Reconstructions/VoxelSpacing13.480/Annotations/115/nucleus-1.0_segmentationmask.zarr,nucleus,,134608,246332
+241,13.48,data-portal,246272,cytoplasm,false,10000/TS_026/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134578,246272
+241,13.48,data-portal,246276,endomembrane,false,10000/TS_026/Reconstructions/VoxelSpacing13.480/Annotations/121/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134580,246276
+241,13.48,data-portal,246274,vesicle,false,10000/TS_026/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134579,246274
+242,13.48,data-portal,246282,nuclear-envelope,false,10000/TS_027/Reconstructions/VoxelSpacing13.480/Annotations/116/nuclear_envelope-1.0_segmentationmask.zarr,nuclear envelope,,134583,246282
+242,13.48,data-portal,246280,nucleus,false,10000/TS_027/Reconstructions/VoxelSpacing13.480/Annotations/115/nucleus-1.0_segmentationmask.zarr,nucleus,,134582,246280
+242,13.48,data-portal,246278,cytoplasm,false,10000/TS_027/Reconstructions/VoxelSpacing13.480/Annotations/114/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134581,246278
+242,13.48,data-portal,246286,endomembrane,false,10000/TS_027/Reconstructions/VoxelSpacing13.480/Annotations/118/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134585,246286
+242,13.48,data-portal,246284,vesicle,false,10000/TS_027/Reconstructions/VoxelSpacing13.480/Annotations/117/vesicle-1.0_segmentationmask.zarr,vesicle,,134584,246284
+243,13.48,data-portal,246290,vesicle,false,10000/TS_028/Reconstructions/VoxelSpacing13.480/Annotations/118/vesicle-1.0_segmentationmask.zarr,vesicle,,134587,246290
+243,13.48,data-portal,246288,cytoplasm,false,10000/TS_028/Reconstructions/VoxelSpacing13.480/Annotations/115/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134586,246288
+243,13.48,data-portal,246292,endomembrane,false,10000/TS_028/Reconstructions/VoxelSpacing13.480/Annotations/119/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134588,246292
+244,13.48,data-portal,246300,mitochondrion,false,10000/TS_029/Reconstructions/VoxelSpacing13.480/Annotations/117/mitochondrion-1.0_segmentationmask.zarr,mitochondrion,,134592,246300
+244,13.48,data-portal,246298,endomembrane,false,10000/TS_029/Reconstructions/VoxelSpacing13.480/Annotations/116/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134591,246298
+244,13.48,data-portal,246296,vesicle,false,10000/TS_029/Reconstructions/VoxelSpacing13.480/Annotations/115/vesicle-1.0_segmentationmask.zarr,vesicle,,134590,246296
+244,13.48,data-portal,246294,cytoplasm,false,10000/TS_029/Reconstructions/VoxelSpacing13.480/Annotations/112/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134589,246294
+245,13.48,data-portal,246302,cytoplasm,false,10000/TS_030/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134593,246302
+245,13.48,data-portal,246306,endomembrane,false,10000/TS_030/Reconstructions/VoxelSpacing13.480/Annotations/121/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134595,246306
+245,13.48,data-portal,246304,vesicle,false,10000/TS_030/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134594,246304
+246,13.48,data-portal,246314,mitochondrion,false,10000/TS_034/Reconstructions/VoxelSpacing13.480/Annotations/122/mitochondrion-1.0_segmentationmask.zarr,mitochondrion,,134599,246314
+246,13.48,data-portal,246312,endomembrane,false,10000/TS_034/Reconstructions/VoxelSpacing13.480/Annotations/121/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134598,246312
+246,13.48,data-portal,246308,cytoplasm,false,10000/TS_034/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134596,246308
+246,13.48,data-portal,246310,vesicle,false,10000/TS_034/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134597,246310
+247,13.48,data-portal,246316,cytoplasm,false,10000/TS_037/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134600,246316
+247,13.48,data-portal,246322,vesicle,false,10000/TS_037/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134603,246322
+247,13.48,data-portal,246320,nuclear-envelope,false,10000/TS_037/Reconstructions/VoxelSpacing13.480/Annotations/119/nuclear_envelope-1.0_segmentationmask.zarr,nuclear envelope,,134602,246320
+247,13.48,data-portal,246318,nucleus,false,10000/TS_037/Reconstructions/VoxelSpacing13.480/Annotations/118/nucleus-1.0_segmentationmask.zarr,nucleus,,134601,246318
+248,13.48,data-portal,246324,cytoplasm,false,10000/TS_041/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134604,246324
+248,13.48,data-portal,246326,vesicle,false,10000/TS_041/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134605,246326
+248,13.48,data-portal,246328,endomembrane,false,10000/TS_041/Reconstructions/VoxelSpacing13.480/Annotations/121/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134606,246328
+250,13.48,data-portal,246344,nuclear-envelope,false,10000/TS_045/Reconstructions/VoxelSpacing13.480/Annotations/116/nuclear_envelope-1.0_segmentationmask.zarr,nuclear envelope,,134614,246344
+250,13.48,data-portal,246348,endomembrane,false,10000/TS_045/Reconstructions/VoxelSpacing13.480/Annotations/118/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134616,246348
+250,13.48,data-portal,246340,cytoplasm,false,10000/TS_045/Reconstructions/VoxelSpacing13.480/Annotations/114/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134612,246340
+250,13.48,data-portal,246346,vesicle,false,10000/TS_045/Reconstructions/VoxelSpacing13.480/Annotations/117/vesicle-1.0_segmentationmask.zarr,vesicle,,134615,246346
+250,13.48,data-portal,246350,mitochondrion,false,10000/TS_045/Reconstructions/VoxelSpacing13.480/Annotations/119/mitochondrion-1.0_segmentationmask.zarr,mitochondrion,,134617,246350
+250,13.48,data-portal,246342,nucleus,false,10000/TS_045/Reconstructions/VoxelSpacing13.480/Annotations/115/nucleus-1.0_segmentationmask.zarr,nucleus,,134613,246342
+253,13.48,data-portal,246376,mitochondrion,false,10001/TS_0003/Reconstructions/VoxelSpacing13.480/Annotations/122/mitochondrion-1.0_segmentationmask.zarr,mitochondrion,,134630,246376
+253,13.48,data-portal,246372,vesicle,false,10001/TS_0003/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134628,246372
+253,13.48,data-portal,246374,endomembrane,false,10001/TS_0003/Reconstructions/VoxelSpacing13.480/Annotations/121/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134629,246374
+253,13.48,data-portal,246370,cytoplasm,false,10001/TS_0003/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134627,246370
+252,13.48,data-portal,246360,cytoplasm,false,10001/TS_0002/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134622,246360
+252,13.48,data-portal,246366,vesicle,false,10001/TS_0002/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134625,246366
+252,13.48,data-portal,246362,nucleus,false,10001/TS_0002/Reconstructions/VoxelSpacing13.480/Annotations/118/nucleus-1.0_segmentationmask.zarr,nucleus,,134623,246362
+252,13.48,data-portal,246364,nuclear-envelope,false,10001/TS_0002/Reconstructions/VoxelSpacing13.480/Annotations/119/nuclear_envelope-1.0_segmentationmask.zarr,nuclear envelope,,134624,246364
+252,13.48,data-portal,246368,endomembrane,false,10001/TS_0002/Reconstructions/VoxelSpacing13.480/Annotations/121/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134626,246368
+254,13.48,data-portal,246378,cytoplasm,false,10001/TS_0004/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134631,246378
+254,13.48,data-portal,246382,endomembrane,false,10001/TS_0004/Reconstructions/VoxelSpacing13.480/Annotations/123/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134633,246382
+254,13.48,data-portal,246384,mitochondrion,false,10001/TS_0004/Reconstructions/VoxelSpacing13.480/Annotations/124/mitochondrion-1.0_segmentationmask.zarr,mitochondrion,,134634,246384
+254,13.48,data-portal,246380,vesicle,false,10001/TS_0004/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134632,246380
+255,13.48,data-portal,246388,vesicle,false,10001/TS_0005/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134636,246388
+255,13.48,data-portal,246386,cytoplasm,false,10001/TS_0005/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134635,246386
+255,13.48,data-portal,246390,endomembrane,false,10001/TS_0005/Reconstructions/VoxelSpacing13.480/Annotations/121/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134637,246390
+256,13.48,data-portal,246400,endomembrane,false,10001/TS_0006/Reconstructions/VoxelSpacing13.480/Annotations/121/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134642,246400
+256,13.48,data-portal,246402,mitochondrion,false,10001/TS_0006/Reconstructions/VoxelSpacing13.480/Annotations/122/mitochondrion-1.0_segmentationmask.zarr,mitochondrion,,134643,246402
+256,13.48,data-portal,246396,nuclear-envelope,false,10001/TS_0006/Reconstructions/VoxelSpacing13.480/Annotations/119/nuclear_envelope-1.0_segmentationmask.zarr,nuclear envelope,,134640,246396
+256,13.48,data-portal,246394,nucleus,false,10001/TS_0006/Reconstructions/VoxelSpacing13.480/Annotations/118/nucleus-1.0_segmentationmask.zarr,nucleus,,134639,246394
+256,13.48,data-portal,246398,vesicle,false,10001/TS_0006/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134641,246398
+256,13.48,data-portal,246392,cytoplasm,false,10001/TS_0006/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134638,246392
+257,13.48,data-portal,246406,nucleus,false,10001/TS_0007/Reconstructions/VoxelSpacing13.480/Annotations/118/nucleus-1.0_segmentationmask.zarr,nucleus,,134645,246406
+257,13.48,data-portal,246412,mitochondrion,false,10001/TS_0007/Reconstructions/VoxelSpacing13.480/Annotations/122/mitochondrion-1.0_segmentationmask.zarr,mitochondrion,,134648,246412
+257,13.48,data-portal,246410,endomembrane,false,10001/TS_0007/Reconstructions/VoxelSpacing13.480/Annotations/121/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134647,246410
+257,13.48,data-portal,246408,nuclear-envelope,false,10001/TS_0007/Reconstructions/VoxelSpacing13.480/Annotations/119/nuclear_envelope-1.0_segmentationmask.zarr,nuclear envelope,,134646,246408
+257,13.48,data-portal,246404,cytoplasm,false,10001/TS_0007/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134644,246404
+258,13.48,data-portal,246416,vesicle,false,10001/TS_0008/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134650,246416
+258,13.48,data-portal,246420,mitochondrion,false,10001/TS_0008/Reconstructions/VoxelSpacing13.480/Annotations/122/mitochondrion-1.0_segmentationmask.zarr,mitochondrion,,134652,246420
+258,13.48,data-portal,246414,cytoplasm,false,10001/TS_0008/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134649,246414
+258,13.48,data-portal,246418,endomembrane,false,10001/TS_0008/Reconstructions/VoxelSpacing13.480/Annotations/121/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134651,246418
+259,13.48,data-portal,246424,nucleus,false,10001/TS_0009/Reconstructions/VoxelSpacing13.480/Annotations/118/nucleus-1.0_segmentationmask.zarr,nucleus,,134654,246424
+259,13.48,data-portal,246422,cytoplasm,false,10001/TS_0009/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134653,246422
+259,13.48,data-portal,246430,endomembrane,false,10001/TS_0009/Reconstructions/VoxelSpacing13.480/Annotations/121/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134657,246430
+259,13.48,data-portal,246426,nuclear-envelope,false,10001/TS_0009/Reconstructions/VoxelSpacing13.480/Annotations/119/nuclear_envelope-1.0_segmentationmask.zarr,nuclear envelope,,134655,246426
+259,13.48,data-portal,246428,vesicle,false,10001/TS_0009/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134656,246428
+251,13.48,data-portal,246354,vesicle,false,10001/TS_0001/Reconstructions/VoxelSpacing13.480/Annotations/120/vesicle-1.0_segmentationmask.zarr,vesicle,,134619,246354
+251,13.48,data-portal,246358,mitochondrion,false,10001/TS_0001/Reconstructions/VoxelSpacing13.480/Annotations/122/mitochondrion-1.0_segmentationmask.zarr,mitochondrion,,134621,246358
+251,13.48,data-portal,246352,cytoplasm,false,10001/TS_0001/Reconstructions/VoxelSpacing13.480/Annotations/117/cytoplasm-1.0_segmentationmask.zarr,cytoplasm,,134618,246352
+251,13.48,data-portal,246356,endomembrane,false,10001/TS_0001/Reconstructions/VoxelSpacing13.480/Annotations/121/membrane_enclosed_lumen-1.0_segmentationmask.zarr,membrane-enclosed lumen,,134620,246356

yeast/Croissant/tomograms.csv

@@ -0,0 +1,21 @@
+run,voxel_size,tomo_type,url,portal_tomo_type,portal_tomogram_id
+249,13.48,wbp-raw,10000/TS_043/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_043.zarr,,629
+241,13.48,wbp-raw,10000/TS_026/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_026.zarr,,621
+242,13.48,wbp-raw,10000/TS_027/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_027.zarr,,622
+243,13.48,wbp-raw,10000/TS_028/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_028.zarr,,623
+244,13.48,wbp-raw,10000/TS_029/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_029.zarr,,624
+245,13.48,wbp-raw,10000/TS_030/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_030.zarr,,625
+246,13.48,wbp-raw,10000/TS_034/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_034.zarr,,626
+247,13.48,wbp-raw,10000/TS_037/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_037.zarr,,627
+248,13.48,wbp-raw,10000/TS_041/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_041.zarr,,628
+250,13.48,wbp-raw,10000/TS_045/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_045.zarr,,630
+253,13.48,wbp-raw,10001/TS_0003/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_0003.zarr,,2271
+252,13.48,wbp-raw,10001/TS_0002/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_0002.zarr,,2270
+254,13.48,wbp-raw,10001/TS_0004/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_0004.zarr,,2272
+255,13.48,wbp-raw,10001/TS_0005/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_0005.zarr,,2273
+256,13.48,wbp-raw,10001/TS_0006/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_0006.zarr,,2274
+257,13.48,wbp-raw,10001/TS_0007/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_0007.zarr,,2275
+258,13.48,wbp-raw,10001/TS_0008/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_0008.zarr,,2276
+259,13.48,wbp-raw,10001/TS_0009/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_0009.zarr,,2277
+260,13.48,wbp-raw,10001/TS_0010/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_0010.zarr,,2278
+251,13.48,wbp-raw,10001/TS_0001/Reconstructions/VoxelSpacing13.480/Tomograms/100/TS_0001.zarr,,2269

yeast/Croissant/voxel_spacings.csv

@@ -0,0 +1,21 @@
+run,voxel_size
+249,13.48
+241,13.48
+242,13.48
+243,13.48
+244,13.48
+245,13.48
+246,13.48
+247,13.48
+248,13.48
+250,13.48
+253,13.48
+252,13.48
+254,13.48
+255,13.48
+256,13.48
+257,13.48
+258,13.48
+259,13.48
+260,13.48
+251,13.48