initial yeast + motorbench

motorbench/Croissant/features.csv

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

motorbench/Croissant/meshes.csv

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

motorbench/Croissant/metadata.json

@@ -0,0 +1,1020 @@
+{
+  "@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 MotorBench",
+  "description": "Single-class bacterial flagellar motor localization benchmark from the POPSICLE suite. Aggregates the BYU 2025 Kaggle challenge training corpus (CZCDP-10332, multi-author community-curated picks across diverse bacterial/archaeal datasets) and the held-out test set (CZCDP-10347, Vibrio cholerae). Picks are filtered by deposition to preserve the train/test boundary defined by the original challenge. Owens et al. (2025), https://doi.org/10.1101/2025.04.23.650258.",
+  "conformsTo": "http://mlcommons.org/croissant/1.1",
+  "version": "1.23.4",
+  "license": "CC0-1.0",
+  "citeAs": "Owens CB et al. (2025). MotorBench: A cryo-electron tomography dataset of bacterial flagellar motors for testing detection algorithms. bioRxiv. doi:10.1101/2025.04.23.650258",
+  "datePublished": "2026-05-05",
+  "copick:baseUrl": "s3://cryoet-data-portal-public/",
+  "copick:config": {
+    "name": "CZ cryoET Data Portal Dataset",
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+    "user_id": null,
+    "session_id": null,
+    "pickable_objects": [
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+        "color": [
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+          0,
+          255
+        ],
+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0009288",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "dense-body",
+        "is_particle": false,
+        "label": 2,
+        "color": [
+          255,
+          0,
+          255,
+          255
+        ],
+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0097433",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "type-iv-secretion-system-complex",
+        "is_particle": true,
+        "label": 3,
+        "color": [
+          0,
+          127,
+          255,
+          255
+        ],
+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0043684",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "membrane",
+        "is_particle": false,
+        "label": 4,
+        "color": [
+          255,
+          127,
+          0,
+          255
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+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0016020",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "bacterial-type-flagellum-basal-body",
+        "is_particle": true,
+        "label": 5,
+        "color": [
+          127,
+          191,
+          127,
+          255
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+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0009425",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "periplasmic-space",
+        "is_particle": false,
+        "label": 6,
+        "color": [
+          94,
+          6,
+          164,
+          255
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+        "emdb_id": null,
+        "pdb_id": null,
+        "identifier": "GO:0042597",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "flagellar-motor",
+        "is_particle": true,
+        "label": 7,
+        "color": [
+          233,
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+          56,
+          255
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+        "pdb_id": null,
+        "identifier": "GO:0120100",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {
+          "portal_original_name": "bacterial-type-flagellum-motor"
+        }
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+        "label": 8,
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+        "pdb_id": null,
+        "identifier": "GO:0044096",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
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+          255,
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+        "pdb_id": null,
+        "identifier": "GO:0005737",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "flagellar-basal-body,-ms-ring",
+        "is_particle": true,
+        "label": 10,
+        "color": [
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+          255
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+        "pdb_id": null,
+        "identifier": "GO:0009431",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "inclusion-body",
+        "is_particle": false,
+        "label": 11,
+        "color": [
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+          74,
+          255
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+        "pdb_id": null,
+        "identifier": "GO:0016234",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      },
+      {
+        "name": "intracellular-anatomical-structure",
+        "is_particle": false,
+        "label": 12,
+        "color": [
+          128,
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+        "pdb_id": null,
+        "identifier": "GO:0005622",
+        "map_threshold": null,
+        "radius": 50.0,
+        "metadata": {}
+      }
+    ]
+  },
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+    {
+      "@type": "cr:FileObject",
+      "@id": "runs-csv",
+      "name": "runs-csv",
+      "contentUrl": "https://huggingface.co/datasets/uermel/popsicle/resolve/main/motorbench/Croissant/runs.csv",
+      "encodingFormat": "text/csv",
+      "sha256": "055c53723f36d40dfe925797236815c60a2a536c69033186d8565989c9b60622"
+    },
+    {
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+      "name": "voxel-spacings-csv",
+      "contentUrl": "https://huggingface.co/datasets/uermel/popsicle/resolve/main/motorbench/Croissant/voxel_spacings.csv",
+      "encodingFormat": "text/csv",
+      "sha256": "ce44bb07f43fce0b7ddce5aef6a4fedc12ff09fb3dda2b6c3992d5947b8744d8"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "tomograms-csv",
+      "name": "tomograms-csv",
+      "contentUrl": "https://huggingface.co/datasets/uermel/popsicle/resolve/main/motorbench/Croissant/tomograms.csv",
+      "encodingFormat": "text/csv",
+      "sha256": "0a353d7c7f7f3495af638896adb44bf9e16f5c30bc417e54b952adf6356de61d"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "features-csv",
+      "name": "features-csv",
+      "contentUrl": "https://huggingface.co/datasets/uermel/popsicle/resolve/main/motorbench/Croissant/features.csv",
+      "encodingFormat": "text/csv",
+      "sha256": "c9d12b09cd878090929fa4e0909e2459257d7b0ec796848d62a90a275d3874ca"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "picks-csv",
+      "name": "picks-csv",
+      "contentUrl": "https://huggingface.co/datasets/uermel/popsicle/resolve/main/motorbench/Croissant/picks.csv",
+      "encodingFormat": "text/csv",
+      "sha256": "3398f9e407c16e7ee6af56655777c6966d7580845106a2e853b36090ed91ea13"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "meshes-csv",
+      "name": "meshes-csv",
+      "contentUrl": "https://huggingface.co/datasets/uermel/popsicle/resolve/main/motorbench/Croissant/meshes.csv",
+      "encodingFormat": "text/csv",
+      "sha256": "236509be0c96d8bc5d7dd79d778dc0343cf79aa0af56ec8b05bfe34c544873e9"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "segmentations-csv",
+      "name": "segmentations-csv",
+      "contentUrl": "https://huggingface.co/datasets/uermel/popsicle/resolve/main/motorbench/Croissant/segmentations.csv",
+      "encodingFormat": "text/csv",
+      "sha256": "bedf5e6be15b7abcab22896f98f0f8dcfab2baa871dff5c0384cc046cb366e5e"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "objects-csv",
+      "name": "objects-csv",
+      "contentUrl": "https://huggingface.co/datasets/uermel/popsicle/resolve/main/motorbench/Croissant/objects.csv",
+      "encodingFormat": "text/csv",
+      "sha256": "86c3b172779c26cb56e1d64eaf039c5bb3e3d7e70977ff2da537a84cbb71a485"
+    }
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+  "recordSet": [
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+      "@id": "copick/runs",
+      "name": "runs",
+      "field": [
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+          "@id": "copick/runs/name",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "runs-csv"
+            },
+            "extract": {
+              "column": "name"
+            }
+          }
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+          "@id": "copick/runs/portal_run_id",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "runs-csv"
+            },
+            "extract": {
+              "column": "portal_run_id"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/runs/split",
+          "dataType": "sc:Text",
+          "source": {
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+            },
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+              "@id": "copick/splits/name"
+            }
+          }
+        }
+      ]
+    },
+    {
+      "@type": "cr:RecordSet",
+      "@id": "copick/voxel_spacings",
+      "name": "voxel_spacings",
+      "field": [
+        {
+          "@type": "cr:Field",
+          "@id": "copick/voxel_spacings/run",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "voxel-spacings-csv"
+            },
+            "extract": {
+              "column": "run"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/voxel_spacings/voxel_size",
+          "dataType": "sc:Float",
+          "source": {
+            "fileObject": {
+              "@id": "voxel-spacings-csv"
+            },
+            "extract": {
+              "column": "voxel_size"
+            }
+          }
+        }
+      ]
+    },
+    {
+      "@type": "cr:RecordSet",
+      "@id": "copick/tomograms",
+      "name": "tomograms",
+      "field": [
+        {
+          "@type": "cr:Field",
+          "@id": "copick/tomograms/run",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "tomograms-csv"
+            },
+            "extract": {
+              "column": "run"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/tomograms/voxel_size",
+          "dataType": "sc:Float",
+          "source": {
+            "fileObject": {
+              "@id": "tomograms-csv"
+            },
+            "extract": {
+              "column": "voxel_size"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/tomograms/tomo_type",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "tomograms-csv"
+            },
+            "extract": {
+              "column": "tomo_type"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/tomograms/url",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "tomograms-csv"
+            },
+            "extract": {
+              "column": "url"
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+        {
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+          "@id": "copick/tomograms/portal_tomo_type",
+          "dataType": "sc:Text",
+          "source": {
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+            },
+            "extract": {
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+        {
+          "@type": "cr:Field",
+          "@id": "copick/tomograms/portal_tomogram_id",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "tomograms-csv"
+            },
+            "extract": {
+              "column": "portal_tomogram_id"
+            }
+          }
+        }
+      ]
+    },
+    {
+      "@type": "cr:RecordSet",
+      "@id": "copick/features",
+      "name": "features",
+      "field": [
+        {
+          "@type": "cr:Field",
+          "@id": "copick/features/run",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "features-csv"
+            },
+            "extract": {
+              "column": "run"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/features/voxel_size",
+          "dataType": "sc:Float",
+          "source": {
+            "fileObject": {
+              "@id": "features-csv"
+            },
+            "extract": {
+              "column": "voxel_size"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/features/tomo_type",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "features-csv"
+            },
+            "extract": {
+              "column": "tomo_type"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/features/feature_type",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "features-csv"
+            },
+            "extract": {
+              "column": "feature_type"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/features/url",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "features-csv"
+            },
+            "extract": {
+              "column": "url"
+            }
+          }
+        }
+      ]
+    },
+    {
+      "@type": "cr:RecordSet",
+      "@id": "copick/picks",
+      "name": "picks",
+      "field": [
+        {
+          "@type": "cr:Field",
+          "@id": "copick/picks/run",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "picks-csv"
+            },
+            "extract": {
+              "column": "run"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/picks/user_id",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "picks-csv"
+            },
+            "extract": {
+              "column": "user_id"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/picks/session_id",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
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+            },
+            "extract": {
+              "column": "session_id"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/picks/object_name",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "picks-csv"
+            },
+            "extract": {
+              "column": "object_name"
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+        {
+          "@type": "cr:Field",
+          "@id": "copick/picks/url",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
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+            },
+            "extract": {
+              "column": "url"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "copick/picks/sha256",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "picks-csv"
+            },
+            "extract": {
+              "column": "sha256"
+            }
+          }
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+          "@id": "copick/picks/portal_object_name",
+          "dataType": "sc:Text",
+          "source": {
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+        {
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+          "@id": "copick/picks/portal_session_id",
+          "dataType": "sc:Text",
+          "source": {
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+              "@id": "picks-csv"
+            },
+            "extract": {
+              "column": "portal_session_id"
+            }
+          }
+        },
+        {
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+          "@id": "copick/picks/portal_annotation_id",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "picks-csv"
+            },
+            "extract": {
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+            }
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+        {
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+          "dataType": "sc:Text",
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+            "fileObject": {
+              "@id": "picks-csv"
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+            "extract": {
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+            }
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