From edf2aefcfeea47062eff8bb6033dd3fe893e0bc5 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Sun, 17 Apr 2022 00:38:24 -0500 Subject: [PATCH 1/7] Add citation section --- README.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/README.md b/README.md index bd2a652..922dad1 100644 --- a/README.md +++ b/README.md @@ -81,3 +81,17 @@ For more detail, check the docstring of the `element-deeplabcut`: ### Example usage See [our workflow](https://github.com/datajoint/workflow-deeplabcut) for an example usage of this DeepLabCut Element. + +## Citation + ++ If your work uses DataJoint and DataJoint Elements, please cite the respective Research Resource Identifiers (RRIDs) and manuscripts. + ++ DataJoint for Python or MATLAB + + Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658 + + + DataJoint ([RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543)) - DataJoint for < Python or MATLAB > (version < enter version number >) + ++ DataJoint Elements + + Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D, Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358 + + + DataJoint Elements ([RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894)) - Element DeepLabCut (version < enter version number >) \ No newline at end of file From e46c6668b1f8d0b3591f94be3736846532c38b24 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Sun, 17 Apr 2022 00:40:01 -0500 Subject: [PATCH 2/7] Add links to elements.datajoint.org --- README.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 922dad1..c4e3d7f 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,22 @@ # DataJoint Element - DeepLabCut -This repository features a DataJoint schema for pose estimation via ***DeepLabCut***. ++ This repository features a DataJoint schema for pose estimation via ***DeepLabCut***. The pipeline presented here is not a complete pipeline by itself, but rather a modular design of tables and dependencies specific to the behavior tracking workflow. This modular pipeline element can be flexibly attached downstream to any particular design of experiment session, thus assembling a fully functional behavior pipeline (see the example [workflow-deeplabcut](https://github.com/datajoint/workflow-deeplabcut)). -This Element currently supports single-animal, single-camera 2D models, and does not yet ++ This Element currently supports single-animal, single-camera 2D models, and does not yet support multi-animal or multi-camera models. This Element does not offer any features for labeling training data. Users should to use native DeepLabCut tools for intitializing a project and labeling training data. -## The Pipeline Architecture ++ See the [Element DeepLabCut documentation](https://elements.datajoint.org/description/deeplabcut/) for the background information and development timeline. + ++ For more information on the DataJoint Elements project, please visit https://elements.datajoint.org. This work is supported by the National Institutes of Health. + +## Element architecture ![element-deeplabcut diagram](images/diagram_dlc.svg) From c7300eb009a7a802edab7c7032e02b1cea18c45b Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Sun, 17 Apr 2022 09:00:54 -0500 Subject: [PATCH 3/7] Fix typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c4e3d7f..1751e36 100644 --- a/README.md +++ b/README.md @@ -68,7 +68,7 @@ To activate the `element-deeplabcut`, one needs to provide: 1. Schema names + optionally, a schema name for the `train` module. - + a schema name for the `model` moduel. + + a schema name for the `model` module. 2. Upstream tables + `Session`: A set of keys identifying a recording session (see [Element-Session](https://github.com/datajoint/element-session)). From 9f39af4d5e1aefbf04dfa537755d9a38748799a2 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Sun, 17 Apr 2022 09:01:16 -0500 Subject: [PATCH 4/7] Fix format --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 1751e36..576ccbe 100644 --- a/README.md +++ b/README.md @@ -82,6 +82,7 @@ For more detail, check the docstring of the `element-deeplabcut`: help(train.activate) help(model.activate) ``` + ### Example usage See [our workflow](https://github.com/datajoint/workflow-deeplabcut) for an example usage of this DeepLabCut Element. From f6311955d6b38b93f701c014ab01193670c5e60e Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Mon, 18 Apr 2022 15:26:07 -0500 Subject: [PATCH 5/7] Update format --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 576ccbe..dcbfaaf 100644 --- a/README.md +++ b/README.md @@ -94,9 +94,9 @@ See [our workflow](https://github.com/datajoint/workflow-deeplabcut) for an exam + DataJoint for Python or MATLAB + Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658 - + DataJoint ([RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543)) - DataJoint for < Python or MATLAB > (version < enter version number >) + + DataJoint ([RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543)) - DataJoint for `