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example data
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@BradyAJohnston
BradyAJohnston committed Jan 10, 2025
1 parent 902b672 commit b5b1b07
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4,152 changes: 4,152 additions & 0 deletions tests/data/cryoet/czii-remapped-points.star
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18 changes: 18 additions & 0 deletions tests/data/cryoet/download.py
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# /// script
# requires-python = ">=3.11"
# dependencies = [
# "cryoet-data-portal",
# ]
# ///
from cryoet_data_portal import (
Client,
Run,
)

client = Client()
run = Run.get_by_id(client, 506)

for annotation in run.annotations:
# Download only ndjson and mrc files
for shape in ["OrientedPoint"]:
annotation.download(shape=shape)
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68 changes: 68 additions & 0 deletions tests/data/cryoet/membrain_seg_prediction-1.0.json
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{
"annotation_method": "Prediction using membrain-seg without rescaling and weights MemBrain_seg_v10_alpha.ckpt",
"annotation_object": {
"description": "Membrain-seg prediction",
"id": "GO:0016020",
"name": "membrane"
},
"annotation_publications": "10.1101/2024.01.05.574336",
"method_links": [
{
"link": "https://github.com/teamtomo/membrain-seg",
"link_type": "source_code",
"custom_name": "membrain-seg on GitHub"
},
{
"link": "https://pypi.org/project/membrain-seg/",
"link_type": "other",
"custom_name": "membrain-seg on PyPI"
},
{
"link": "https://github.com/uermel/remotebrain",
"link_type": "source_code",
"custom_name": "remotebrain on GitHub"
}
],
"annotation_software": "membrain-seg 0.0.1",
"authors": [
{
"ORCID": "0000-0003-4685-037X",
"corresponding_author_status": true,
"name": "Utz Heinrich Ermel",
"primary_author_status": true
},
{
"ORCID": "0000-0002-7237-1973",
"corresponding_author_status": false,
"name": "Kyle I. S. Harrington",
"primary_author_status": false
}
],
"dates": {
"deposition_date": "2024-05-20",
"last_modified_date": "2024-05-20",
"release_date": "2024-05-20"
},
"ground_truth_status": false,
"is_curator_recommended": false,
"method_type": "automated",
"version": 1.0,
"object_count": 0,
"files": [
{
"format": "zarr",
"path": "10006/TS_057/Reconstructions/VoxelSpacing6.128/Annotations/102/membrain_seg_prediction-1.0_segmentationmask.zarr",
"shape": "SegmentationMask",
"is_visualization_default": true
},
{
"format": "mrc",
"path": "10006/TS_057/Reconstructions/VoxelSpacing6.128/Annotations/102/membrain_seg_prediction-1.0_segmentationmask.mrc",
"shape": "SegmentationMask",
"is_visualization_default": true
}
],
"deposition_id": 10303,
"last_updated_at": 1725501797,
"alignment_metadata_path": "10006/TS_057/Alignments/100/alignment_metadata.json"
}
64 changes: 64 additions & 0 deletions tests/data/cryoet/membrane-1.0.json
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{
"annotation_method": "intensity normalization + rescaling + FNET segmentation + skeletonization + DIST segmentation",
"annotation_object": {
"id": "GO:0016020",
"name": "membrane"
},
"annotation_software": "TARDIS",
"annotation_publications": "10.1093/micmic/ozad067.485",
"method_links": [
{
"link": "https://github.com/SMLC-NYSBC/TARDIS",
"link_type": "source_code",
"custom_name": "TARDIS on GitHub"
},
{
"link": "https://smlc-nysbc.github.io/TARDIS/",
"link_type": "documentation",
"custom_name": "TARDIS documentation"
}
],
"authors": [
{
"name": "Robert Kiewisz",
"primary_author_status": true
},
{
"corresponding_author_status": true,
"name": "Tristan Bepler"
}
],
"dates": {
"deposition_date": "2024-02-20",
"last_modified_date": "2024-02-20",
"release_date": "2024-02-20"
},
"ground_truth_status": false,
"is_curator_recommended": false,
"method_type": "automated",
"version": 1.0,
"object_count": 14,
"files": [
{
"format": "ndjson",
"path": "10006/TS_057/Reconstructions/VoxelSpacing6.128/Annotations/101/membrane-1.0_instancesegmentation.ndjson",
"shape": "InstanceSegmentation",
"is_visualization_default": false
},
{
"format": "zarr",
"path": "10006/TS_057/Reconstructions/VoxelSpacing6.128/Annotations/101/membrane-1.0_segmentationmask.zarr",
"shape": "SegmentationMask",
"is_visualization_default": false
},
{
"format": "mrc",
"path": "10006/TS_057/Reconstructions/VoxelSpacing6.128/Annotations/101/membrane-1.0_segmentationmask.mrc",
"shape": "SegmentationMask",
"is_visualization_default": false
}
],
"deposition_id": 10301,
"last_updated_at": 1725498750,
"alignment_metadata_path": "10006/TS_057/Alignments/100/alignment_metadata.json"
}
83 changes: 0 additions & 83 deletions tests/data/cryoet/point.ndjson
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100 changes: 100 additions & 0 deletions tests/data/cryoet/sars_cov2_spike_protein-1.0.json
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{
"annotation_method": "Template matching + 3D classification filtering",
"annotation_object": {
"description": "SARS-CoV2 Spike protein",
"id": "GO:0044423",
"name": "SARS-CoV2 spike protein"
},
"annotation_publications": "doi:10.1038/s41586-020-2665-2",
"annotation_software": "TOM/AV3 + RELION",
"authors": [
{
"ORCID": "0000-0002-8408-850X",
"name": "Zunlong Ke",
"primary_author_status": true
},
{
"ORCID": "0000-0002-2195-4730",
"name": "Joaquin Oton",
"primary_author_status": true
},
{
"ORCID": "0000-0002-3152-2237",
"name": "Kun Qu",
"primary_author_status": true
},
{
"ORCID": "0000-0003-1786-4211",
"name": "Mirko Cortese"
},
{
"ORCID": "0000-0003-2032-3600",
"name": "Vojtech Zila"
},
{
"name": "Lesley McKeane"
},
{
"ORCID": "0000-0003-2697-2767",
"name": "Takanori Nakane"
},
{
"name": "Jasenko Zivanov"
},
{
"ORCID": "0000-0002-4551-1811",
"name": "Christopher Neufeldt"
},
{
"name": "Berati Cerikan"
},
{
"ORCID": "0000-0002-3972-8854",
"name": "John Lu"
},
{
"ORCID": "0000-0001-8560-7407",
"name": "Julia Peukes"
},
{
"ORCID": "0000-0002-4632-9122",
"name": "Xiaoli Xiong"
},
{
"name": "Hans-Georg Kr\u00e4usslich"
},
{
"ORCID": "0000-0002-0462-6540",
"name": "Sjors H. W. Scheres"
},
{
"ORCID": "0000-0001-5601-9307",
"name": "Ralf Bartenschlager"
},
{
"ORCID": "0000-0003-3990-6910",
"corresponding_author_status": true,
"name": "John Briggs"
}
],
"dates": {
"deposition_date": "2023-10-11",
"last_modified_date": "2023-11-20",
"release_date": "2023-12-10"
},
"ground_truth_status": true,
"is_curator_recommended": true,
"method_type": "hybrid",
"version": 1.0,
"object_count": 52,
"files": [
{
"format": "ndjson",
"path": "10006/TS_057/Reconstructions/VoxelSpacing6.128/Annotations/100/sars_cov2_spike_protein-1.0_orientedpoint.ndjson",
"shape": "OrientedPoint",
"is_visualization_default": true
}
],
"deposition_id": 10006,
"alignment_metadata_path": "10006/TS_057/Alignments/100/alignment_metadata.json"
}
0 tests/data/cryoet/oriented_point.ndjson → ...v2_spike_protein-1.0_orientedpoint.ndjson
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