User documentation about the MicroCT Data API.
To upload a micro-CT dataset please register first.
API
Introduction
Welcome to the MicroCT data API. You can use the API to access microCT API endpoints, which can get information on various microCT data scans, species and metadata info related with the microCT dataset scans.
Species
This endpoint retrieves all species.
HTTP Request
GET taxonomy/species/all?_format=hal_jsonAPI Request Result
[
{
"tid": "63",
"name": "Mollusca",
"parent_target_name": "",
"parent_target_tid": ""
},
{
"tid": "64",
"name": "Bivalvia",
"parent_target_name": "Mollusca",
"parent_target_tid": "63"
},
{
"tid": "65",
"name": "Mytiloida",
"parent_target_name": "Bivalvia",
"parent_target_tid": "64"
},
{
"tid": "66",
"name": "Mytilidae",
"parent_target_name": "Mytiloida",
"parent_target_tid": "65"
},
{
"tid": "67",
"name": "Musculus",
"parent_target_name": "Mytilidae",
"parent_target_tid": "66"
},
{
"tid": "68",
"name": "Musculus costulatus",
"parent_target_name": "Musculus",
"parent_target_tid": "67"
},
{
"tid": "69",
"name": "Arthropoda",
"parent_target_name": "",
"parent_target_tid": ""
},
{
"tid": "70",
"name": "Malacostraca",
"parent_target_name": "Arthropoda",
"parent_target_tid": "69"
},
{
"tid": "71",
"name": "Isopoda",
"parent_target_name": "Malacostraca",
"parent_target_tid": "70"
},
{
"tid": "72",
"name": "Chordata",
"parent_target_name": "",
"parent_target_tid": ""
},
{
"tid": "73",
"name": "Actinopteri",
"parent_target_name": "Chordata",
"parent_target_tid": "72"
},
{
"tid": "74",
"name": "Perciformes",
"parent_target_name": "Actinopteri",
"parent_target_tid": "73"
},
{
"tid": "75",
"name": "Sparidae",
"parent_target_name": "Perciformes",
"parent_target_tid": "74"
},
{
"tid": "76",
"name": "Maxillopoda",
"parent_target_name": "Arthropoda",
"parent_target_tid": "69"
},
{
"tid": "77",
"name": "Calanoida",
"parent_target_name": "Maxillopoda",
"parent_target_tid": "76"
},
{
"tid": "78",
"name": "Calanidae",
"parent_target_name": "Calanoida",
"parent_target_tid": "77"
},
{
"tid": "79",
"name": "Calanus",
"parent_target_name": "Calanidae",
"parent_target_tid": "78"
},
{
"tid": "80",
"name": "Echinodermata",
"parent_target_name": "",
"parent_target_tid": ""
},
{
"tid": "84",
"name": "Polychaeta",
"parent_target_name": "Annelida",
"parent_target_tid": "83"
},
{
"tid": "85",
"name": "Eunicida",
"parent_target_name": "Polychaeta",
"parent_target_tid": "84"
},
{
"tid": "86",
"name": "Eunicidae",
"parent_target_name": "Eunicida",
"parent_target_tid": "85"
},
{
"tid": "87",
"name": "Eunice",
"parent_target_name": "Eunicidae",
"parent_target_tid": "86"
},
{
"tid": "88",
"name": "Amphinomida",
"parent_target_name": "Polychaeta",
"parent_target_tid": "84"
},
{
"tid": "89",
"name": "Amphinomidae",
"parent_target_name": "Amphinomida",
"parent_target_tid": "88"
},
{
"tid": "90",
"name": "Hermodice",
"parent_target_name": "Amphinomidae",
"parent_target_tid": "89"
},
{
"tid": "91",
"name": "Hermodice carunculata",
"parent_target_name": "Hermodice",
"parent_target_tid": "90"
},
{
"tid": "92",
"name": "Lumbrineridae",
"parent_target_name": "Eunicida",
"parent_target_tid": "85"
},
{
"tid": "93",
"name": "Lumbrineris",
"parent_target_name": "Lumbrineridae",
"parent_target_tid": "92"
},
{
"tid": "94",
"name": "Lumbrineris latreilli",
"parent_target_name": "Lumbrineris",
"parent_target_tid": "93"
},
{
"tid": "95",
"name": "Phyllodocida",
"parent_target_name": "Polychaeta",
"parent_target_tid": "84"
},
{
"tid": "96",
"name": "Phyllodocidae",
"parent_target_name": "Phyllodocida",
"parent_target_tid": "95"
},
{
"tid": "97",
"name": "Phyllodoce",
"parent_target_name": "Phyllodocidae",
"parent_target_tid": "96"
},
{
"tid": "98",
"name": "Phyllodoce lineata",
"parent_target_name": "Phyllodoce",
"parent_target_tid": "97"
},
{
"tid": "99",
"name": "Nereididae",
"parent_target_name": "Phyllodocida",
"parent_target_tid": "95"
},
{
"tid": "100",
"name": "Alitta",
"parent_target_name": "Nereididae",
"parent_target_tid": "99"
},
{
"tid": "101",
"name": "Alitta succinea",
"parent_target_name": "Alitta",
"parent_target_tid": "100"
},
{
"tid": "102",
"name": "Syllidae",
"parent_target_name": "Phyllodocida",
"parent_target_tid": "95"
},
{
"tid": "103",
"name": "Syllis",
"parent_target_name": "Syllidae",
"parent_target_tid": "102"
},
{
"tid": "104",
"name": "Syllis gracilis",
"parent_target_name": "Syllis",
"parent_target_tid": "103"
},
{
"tid": "105",
"name": "Gastropoda",
"parent_target_name": "Mollusca",
"parent_target_tid": "63"
},
{
"tid": "106",
"name": "Neogastropoda",
"parent_target_name": "Gastropoda",
"parent_target_tid": "105"
},
{
"tid": "107",
"name": "Nassariidae",
"parent_target_name": "Neogastropoda",
"parent_target_tid": "106"
},
{
"tid": "108",
"name": "Nassarius",
"parent_target_name": "Nassariidae",
"parent_target_tid": "107"
},
{
"tid": "109",
"name": "Nassarius nitidus",
"parent_target_name": "Nassarius",
"parent_target_tid": "108"
},
{
"tid": "110",
"name": "Ochrophyta",
"parent_target_name": "",
"parent_target_tid": ""
},
{
"tid": "111",
"name": "Phaeophyceae",
"parent_target_name": "Ochrophyta",
"parent_target_tid": "110"
}
],
Get all the microCT scanned datasets from a Specific Specie
This endpoint retrieves all the microCT datasets from a Specific Species
HTTP Request
GET taxonomy/species/microct-datasets/[id]?_format=hal_jsonURL Parameters
| Parameter | Description |
| ID | The ID of the specie to retrieve |
[
{
"nid": "17",
"view_node": "<a href="http://127.0.0.1:8888/microct8/web/dataset/musculus-costulatus-bivalvia" hreflang="und">view</a>",
"title": "Musculus costulatus (Bivalvia)"
},
{
"nid": "33",
"view_node": "<a href="http://127.0.0.1:8888/microct8/web/dataset/nassarius-nitidus-gastropoda" hreflang="und">view</a>",
"title": "Nassarius nitidus (Gastropoda)"
}
],
Get a specific microCT scanned dataset
HTTP Request
GET /node/[dataset-id]?_format=hal_jsonApi Request Result
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/dataset/musculus-costulatus-bivalvia?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/node/mcdataset"
},
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/revision_uid": [
{
"href": "http://127.0.0.1:8888/microct8/web/user/0?_format=hal_json"
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/uid": [
{
"href": "http://127.0.0.1:8888/microct8/web/user/17?_format=hal_json",
"lang": "und"
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_contrastenhancementmethod": [
{
"href": "http://127.0.0.1:8888/microct8/web/contrast-enhancement-method/pta?_format=hal_json"
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_digital_device_type": [
{
"href": "http://127.0.0.1:8888/microct8/web/digital-device-type/skyscan-1172?_format=hal_json"
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_image": [
{
"href": "http://127.0.0.1:8888/microct8/web/file/44?_format=hal_json"
},
{
"href": "http://127.0.0.1:8888/microct8/web/file/103?_format=hal_json"
},
{
"href": "http://127.0.0.1:8888/microct8/web/file/105?_format=hal_json"
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_metadata_filter": [
{
"href": "http://127.0.0.1:8888/microct8/web/metadata-filter/none?_format=hal_json"
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_nifti_file": [
{
"href": "http://127.0.0.1:8888/microct8/web/file/45?_format=hal_json"
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_species": [
{
"href": "http://127.0.0.1:8888/microct8/web/species/mollusca?_format=hal_json"
},
{
"href": "http://127.0.0.1:8888/microct8/web/species/bivalvia?_format=hal_json"
},
{
"href": "http://127.0.0.1:8888/microct8/web/species/mytiloida?_format=hal_json"
},
{
"href": "http://127.0.0.1:8888/microct8/web/species/mytilidae?_format=hal_json"
},
{
"href": "http://127.0.0.1:8888/microct8/web/species/musculus?_format=hal_json"
},
{
"href": "http://127.0.0.1:8888/microct8/web/species/musculus-costulatus?_format=hal_json"
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_video_file": [
{
"href": "http://127.0.0.1:8888/microct8/web/file/46?_format=hal_json"
}
]
},
"nid": [
{
"value": 17
}
],
"uuid": [
{
"value": "eac30147-93b6-43de-acbd-ee402466642e"
}
],
"vid": [
{
"value": 17
}
],
"langcode": [
{
"value": "und",
"lang": "und"
}
],
"type": [
{
"target_id": "mcdataset"
}
],
"revision_timestamp": [
{
"value": "2020-07-16T08:26:16+00:00",
"format": "Y-m-d\\TH:i:sP"
}
],
"_embedded": {
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/revision_uid": [
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/user/0?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/user/user"
}
},
"uuid": [
{
"value": "ebf30b12-b38a-440e-9b08-735f6489f40b"
}
]
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/uid": [
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/user/17?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/user/user"
}
},
"uuid": [
{
"value": "83c2c110-8bf2-4f18-a44f-2e59625797b4"
}
],
"lang": "und"
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_contrastenhancementmethod": [
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/contrast-enhancement-method/pta?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/taxonomy_term/contrast_enhancement_method"
}
},
"uuid": [
{
"value": "b55af2dc-c5bb-44bb-a564-9de4a52e4941"
}
]
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_digital_device_type": [
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/digital-device-type/skyscan-1172?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/taxonomy_term/digital_device_type"
}
},
"uuid": [
{
"value": "a04c12f9-551b-44cd-8300-a29761d76c4e"
}
]
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_image": [
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/file/44?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/file/image"
}
},
"uuid": [
{
"value": "893b1fd4-11b7-4561-bbc3-8031b0b61b70"
}
],
"alt": "",
"title": "",
"width": "1389",
"height": "969"
},
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/file/103?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/file/image"
}
},
"uuid": [
{
"value": "051b4e09-e37d-4a7a-9a5a-c26f76fd2fe7"
}
],
"alt": "",
"title": "",
"width": "1624",
"height": "1009"
},
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/file/105?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/file/image"
}
},
"uuid": [
{
"value": "6c3ead86-e576-4be9-8660-39fdd44a7a87"
}
],
"alt": "",
"title": "",
"width": "1624",
"height": "1009"
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_metadata_filter": [
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/metadata-filter/none?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/taxonomy_term/metadata_filter"
}
},
"uuid": [
{
"value": "83a8da20-d50b-4bf4-9d5f-4d902e738da5"
}
]
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_nifti_file": [
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/file/45?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/file/undefined"
}
},
"uuid": [
{
"value": "6b44c263-98ad-4c19-a3a2-2434a78276cc"
}
],
"display": "1",
"description": "",
"alt": "",
"title": ""
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_species": [
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/species/mollusca?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/taxonomy_term/species"
}
},
"uuid": [
{
"value": "a44bc99b-cb61-4120-9d69-9ff96ac68f37"
}
]
},
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/species/bivalvia?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/taxonomy_term/species"
}
},
"uuid": [
{
"value": "13e51a81-b693-4846-872d-89ecb3850928"
}
]
},
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/species/mytiloida?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/taxonomy_term/species"
}
},
"uuid": [
{
"value": "f979df24-163e-402b-959b-058d7f40bd0f"
}
]
},
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/species/mytilidae?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/taxonomy_term/species"
}
},
"uuid": [
{
"value": "076e97d7-3c09-48fb-a31e-6b87e7a4a2f2"
}
]
},
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/species/musculus?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/taxonomy_term/species"
}
},
"uuid": [
{
"value": "a1918fd7-aa33-41d5-8a10-6939ff1504b7"
}
]
},
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/species/musculus-costulatus?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/taxonomy_term/species"
}
},
"uuid": [
{
"value": "e5700b3c-dd9d-4246-bc6f-398b0b5f991a"
}
]
}
],
"http://127.0.0.1:8888/microct8/web/rest/relation/node/mcdataset/field_video_file": [
{
"_links": {
"self": {
"href": "http://127.0.0.1:8888/microct8/web/file/46?_format=hal_json"
},
"type": {
"href": "http://127.0.0.1:8888/microct8/web/rest/type/file/video"
}
},
"uuid": [
{
"value": "10ce4732-ab95-4db7-a5ce-b434410ebfb9"
}
],
"display": "1",
"description": "",
"alt": "",
"title": ""
}
]
},
"status": [
{
"value": true,
"lang": "und"
}
],
"title": [
{
"value": "Musculus costulatus (Bivalvia)",
"lang": "und"
}
],
"created": [
{
"value": "2015-07-23T10:26:51+00:00",
"lang": "und",
"format": "Y-m-d\\TH:i:sP"
}
],
"changed": [
{
"value": "2021-01-26T21:04:01+00:00",
"lang": "und",
"format": "Y-m-d\\TH:i:sP"
}
],
"promote": [
{
"value": true,
"lang": "und"
}
],
"sticky": [
{
"value": false,
"lang": "und"
}
],
"default_langcode": [
{
"value": true,
"lang": "und"
}
],
"revision_translation_affected": [
{
"value": true,
"lang": "und"
}
],
"path": [
{
"alias": "/dataset/musculus-costulatus-bivalvia",
"pid": 1,
"langcode": "und",
"lang": "und"
}
],
"body": [
{
"value": "<p>Micro-CT was performed to a small bivalve <em>Musculus costulatus</em>. This specimen was fixed and preserved in 96% ethanol. Specimen was stained in 0.3% PTA solution in 70% ethanol for 5 days. Scan was performed with a Skyscan 1172 at a voltage of 59kV and 167μΑ without filter for a full rotation of 360<sup>o</sup> . This specimen was scanned at the highest camera resolution with an exposure time of 1555ms. This scan was performed for testing contrast enhancing techniques for the application of micro-CT in marine biodiversity studies (http://www.microscopy-analysis.com/sites/default/files/2013_March_Faulwetter.pdf). Specimen was provided and scanned by Sarah Faulwetter.</p>\r\n",
"format": "filtered_html",
"processed": "<p>Micro-CT was performed to a small bivalve <em>Musculus costulatus</em>. This specimen was fixed and preserved in 96% ethanol. Specimen was stained in 0.3% PTA solution in 70% ethanol for 5 days. Scan was performed with a Skyscan 1172 at a voltage of 59kV and 167μΑ without filter for a full rotation of 360<sup>o</sup> . This specimen was scanned at the highest camera resolution with an exposure time of 1555ms. This scan was performed for testing contrast enhancing techniques for the application of micro-CT in marine biodiversity studies (<a href=\"http://www.microscopy-analysis.com/sites/default/files/2013_March_Faulwetter.pdf\">http://www.microscopy-analysis.com/sites/default/files/2013_March_Faulw…</a>). Specimen was provided and scanned by Sarah Faulwetter.</p>\n",
"summary": ""
}
],
"field_description_mobile": [
{
"value": "<em>Musculus costulatus</em> is a marine bivalve mollusk which belong to Mytilidae family. This bivalve attach to the surfaces using their strong byssus. They are filter feeders and they live south to the Mediterranean and north-west Africa. Specimen provided by Sarah Faulwetter (HCMR)."
}
],
"field_exposuretime_ms": [
{
"value": 1555
}
],
"field_mobile_version": [
{
"value": true
}
],
"field_scandate": [
{
"value": "2012-01-23T20:41:00+00:00",
"format": "Y-m-d\\TH:i:sP"
}
],
"field_scanid": [
{
"value": "scan-00184"
}
],
"field_scannedby": [
{
"value": "Sarah Faulwetter"
}
],
"field_scanningevent_id": [
{
"value": "scan-00184"
}
],
"field_sname": [
{
"value": "<i>Musculus costulatus</i>",
"format": "filtered_html",
"processed": "<p><i>Musculus costulatus</i></p>\n"
}
],
"field_specimenid": [
{
"value": "mCT-00162"
}
],
"field_voltage_kv": [
{
"value": 59
}
],
"field_zoom_um": [
{
"value": "1.28"
}
]
}
