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White", "type": "personal" } }, { "affiliations": [ { "name": "The Jackson Laboratory" } ], "person_or_org": { "family_name": "Elissa J. Chesler", "name": "Elissa J. Chesler", "type": "personal" } }, { "affiliations": [ { "name": "The Jackson Laboratory" } ], "person_or_org": { "family_name": "Cathleen M. Lutz", "name": "Cathleen M. Lutz", "type": "personal" } }, { "affiliations": [ { "name": "The Jackson Laboratory" } ], "person_or_org": { "family_name": "Vivek Kumar", "identifiers": [ { "identifier": "0000-0001-6643-7465", "scheme": "orcid" } ], "name": "Vivek Kumar", "type": "personal" } } ], "description": "
Both the training data and trained models used in the paper are found here.
\n\nDataset description
\n\nInformation for each dataset falls into 3 folders. Filenames portray the dataset split used in the paper that they belong to (eg Training_1.png or Validation_1.png).
\n\nTrained Model Description
\n\nWe also release models trained on all the subsets of training data we share. Each trained model was trained using our code over on Github: https://github.com/KumarLabJax/MouseTracking
\n\nBrief descriptions of the training subsets
\n\nPlease read the associated paper for additional detail. A brief summary of the environment is added here:
\n\nStandard Open Field Strain Survey
\n\nWe annotated 16234 training and 568 validation images of a single mouse in the same open field. The mouse can be one of multiple coat colors, but visually appears as a black, light-grey, or white color. In the case the mouse’s posture created a poor ellipse-fit, portions of the mouse were removed (such as tail) to enable a good ellipse-fit.
\n\n24Hr Open Field Dataset
\n\nWe annotated 2099 training and 93 validation images of a single mouse in the same open field listed above augmented with bedding and a food container. All mice in this experiment appear black on video. There are 2 states, with visible light and with only infrared. The infrared-only imaging contains much higher visual noise.
\n\nKOMP Open Field Dataset
\n\nWe annotated 1000 training and 83 validation images of a single mouse in JAX’s KOMP2 open field arena. All mice have a black coat color.
\n\nTest Ground Truth Dataset
\n\nTo test the robustness of our system against conventional trackers that build a background model from multiple frames in a video, we re-sampled video a 20 minute video at 1 frame per second and annotated all the resulting frames (1179-1200 frames). We did this for the 6 environments in the paper of varying difficulty (Black, Gray, Piebald, Albino, 24Hr, KOMP2). The format of this data follows a DataSubset_FrameNumber format instead of Training/Validation_FrameNumber format.
", "publication_date": "2019-03-29", "publisher": "Zenodo", "references": [ { "reference": "Geuther, Brian Q., et al. \"Robust mouse tracking in complex environments using neural networks.\" Communications biology 2.1 (2019): 1-11." } ], "resource_type": { "id": "publication-article", "title": { "de": "Zeitschriftenartikel", "en": "Journal article" } }, "rights": [ { "description": { "en": "" }, "icon": "cc-by-nc-nd-icon", "id": "cc-by-nc-nd-4.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode" }, "title": { "en": "Creative Commons Attribution Non Commercial No Derivatives 4.0 International" } } ], "subjects": [ { "subject": "mouse" }, { "subject": "segmentation" } ], "title": "Robust mouse tracking in complex environments using neural networks" }, "parent": { "access": { "owned_by": { "user": 207411 } }, "communities": {}, "id": "5806396", "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.5806396", "provider": "datacite" } } }, "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.5806397", "provider": "datacite" }, "oai": { "identifier": "oai:zenodo.org:5806397", "provider": "oai" } }, "revision_id": 2, "stats": { "all_versions": { "data_volume": 1323765954560.0, "downloads": 1633, "unique_downloads": 415, "unique_views": 491, "views": 551 }, "this_version": { "data_volume": 1323581736960.0, "downloads": 1632, "unique_downloads": 414, "unique_views": 490, "views": 549 } }, "status": "published", "updated": "2021-12-28T13:48:42.739012+00:00", "versions": { "index": 1, "is_latest": true } }