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Additional information can be found on the [[/Discussion|Discussion]] page.
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<<TableOfContents>>
= Overview =
Open Knee(s) project will generate a plethora of heterogeneous data sets, e.g. DICOM images, joint/tissue mechanical testing data, etc. It is unnecessary and sometimes clumsy to put the data into source code repositories. The workflow of the "Downloads" section at the project site also seems cumbersome for intermediate storage of data, which may not be release ready. This specification is targeted to find a solution for online curation and storage of data (in-house or at Open Knee(s) project site) that will accommodate the workflow of data collection, analysis, and public release. A separate project site at SimTK.org is available to expand management of data and relevant information for biomechanics studies beyond the realm of Open Knee(s), see https://simtk.org/home/dmmb.
= Target Outcome =
Curation and storage of specimen/sample associated data for discoverability, retrieval, and dissemination
= Prerequisites =
== Infrastructure ==
* A data management system, e.g. [[http://www.midasplatform.org/|Midas Platform]], for data curation.
* A dissemination platform, e.g. Downloads section of [[https://simtk.org/home/openknee]], also see [[Infrastructure/Collaboration]]
== Previous Protocols ==
* [[Specifications/Specimens]]
* [[Specifications/SpecimenPreparation]]
== Related Protocols ==
Any experimentation protocol, see:
* [[Specifications/ExperimentationAnatomicalImaging]]
* [[Specifications/ExperimentationJointMechanics]]
* [[Specifications/ExperimentationTissueMechanics]]
= Protocols =
== Specimen/Sample Labeling ==
=== Joint ===
Whole knee specimen labels include the Open Knee(s) abbreviation in lower case, oks, immediately followed by three numerals to indicate specimen number, e.g. 001. An example for knee specimen labeling is in following:
oks001:: Open Knee(s) Specimen 1
=== Tissue ===
Tissue testing plans of Open Knee(s) will require a large set of tissue samples acquired from a single knee specimen; see details in [[Specifications/SpecimenPreparation]] and [[Specifications/ExperimentationTissueMechanics]]. For example, confined and unconfined compression testing of cartilage will require a total of 10 samples from medial and lateral sides of femur and tibia, and from patella. Compression and tension testing of menisci will require a total of 4 samples from medial and lateral sides. Uniaxial tension testing of ligaments and tendons will require a total of 6 samples from their midsubstance (cruciate, collateral, and patellar ligaments, quadriceps tendon). For a single knee, a total of 20 tissue samples may need to acquired, indicating a need for organization of samples and accompanying data.
Labels for tissue samples include knee specimen label, e.g. oks002, followed by three letter tissue type in upper case, e.g. TBC, four letter tissue location in upper case (from gross to granular location, lower case if at microscale), and two numerals to indicate sample number. When needed, the character ''X'' is used as a filler. A few examples for tissue samples are in following:
oks001-PTC-MCXX-02:: sample 2 from patellar cartilage of Open Knee(s) Specimen 1, acquired from the medial side at the center.
oks002-MNS-MAvX-01:: sample 1 from medial meniscus of Open Knee(s) Specimen 2, acquired from middle layer of the tissue at the anterior side.
==== Tissue Types ====
* Bone
* '''FMB''': femur
* '''TBB''': tibia
* '''FBB''': fibula
* '''PTB''': patella
* Cartilage
* '''FMC''': femoral cartilage
* '''TBC''': tibial cartilage
* '''PTC''': patellar cartilage
* Meniscus
* '''MNS''': meniscus
* Ligament
* '''ACL''': anterior cruciate ligament
* '''PCL''': posterior cruciate ligament
* '''MCL''': medial collateral ligament
* '''LCL''': lateral collateral ligament
* '''PTL''': patellar ligament
* Tendon
* '''QAT''': quadriceps tendon
* Secondary Tissues
* '''SMT''': Semitendinosus
* '''MPL''': Medial patellofemoral ligament
* '''LPL''': Lateral patellofemoral ligament
* '''MCP''': Medial tibiofemoral capsule
* '''LCP''': lateral tibiofemoral capsule
* '''BRS''': Fat bursa
* '''TRL''': Transverse ligament
==== Tissue Locations ====
The tissue location is labeled starting from its gross location and ending with its granular position.
* Bone
* '''M''' or '''L''': medial or lateral
* '''A''' or '''P''': anterior or posterior
* '''S''' or '''I''': superior or inferior
* '''C''': central
* Cartilage
* '''M''' or '''L''': medial or lateral
* '''A''' or '''P''': anterior or posterior
* '''C''': central
* '''u''' or '''v''' or '''w''': superficial or transitional or deep zone
* Meniscus
* '''M''' or '''L''': medial or lateral
* '''A''' or '''P''': anterior or posterior
* '''C''': central
* '''u''' or '''v''' or '''w''': femur side or mid-substance or tibia side
* Ligament
* '''S''' or '''I''' or '''C''': superior or inferior or central
* Tendon
* '''S''' or '''I''' or '''C''': superior or inferior or central
Examples (only tissue type and tissue location are shown):
FMC-MAXX:: femoral cartilage sample acquired medially and anteriorly
TBC-LAuX:: tibial cartilage sample acquired laterally and anteriorly from the superficial zone
FMC-AXXX:: femoral cartilage sample acquired from the trochlear groove
MNS-LCwX:: sample acquired from lateral meniscus centrally and from mid-substance
MCL-IXXX:: medial collateral ligament sample acquired from inferior region
{{attachment:t_loc-labels.png}}
== Model Labeling ==
Model geometry is derived from MR image data. Therefore, model component labeling should include the specific MR image set/protocol from which the model geometry is derived. The proposed model labeling convention extends and utilizes the Specimen/Sample Labeling convention to specify the model component (but only uses one character to specify model component/tissue sub-location instead of four, e.g. -M, medial; -L, lateral; -S, superior; etc.).
=== Segmentation ===
==== MRI ====
* '''MRG''': General Purpose MRI (MR-, for MRI; -G, for General Purpose)
* '''MRC''': Cartilage MRI, sagittal in-plane orientation
* '''MRL-s''': Ligament/tendon (connective tissue) MRI, sagittal in-plane orientation
* '''MRL-c''': Ligament/tendon (connective tissue) MRI, coronal in-plane orientation
* '''MRL-a''': Ligament/tendon (connective tissue) MRI, axial in-plane orientation
==== Registration Markers ====
* '''FMR''': Femur registration marker (FM-, for femur; -R, for registration marker/sphere)
* '''-P''': posterior sphere
* '''-L''': lateral sphere
* '''-M''': medial sphere
* '''TBR''': Tibia registration marker
* '''-P''': posterior sphere
* '''-L''': lateral sphere
* '''-M''': medial sphere
* '''PTR''': Patella registration marker
* '''-S''': superior sphere
* '''-L''': lateral sphere
* '''-M''': medial sphere
==== Tissue Type/Location ====
* ''see Specimen/Sample Labeling''
Examples:
oks001_MRG_FMR-P_01.nii:: oks001 specimen, general purpose MRI, posterior femur registration marker sphere, version 1, NifTI image
oks001_MRC_MNS-L.nii:: oks001, cartilage MRI, lateral meniscus, NifTI image
oks001_MRL-s_PTR-S_03.nii:: oks001, sagittal ligament/tendon (connective tissue) MRI, superior patella registration marker sphere, version 3, NifTI image
==== Organization of Authors ====
When segmenting, record the three letter initials of the segmentor (use an X if no middle name) after the tissue description and before the version number, separated by underscores.
Example:
oks001_MRG_FMR-P_JPS_01.nii:: oks001 specimen, general purpose MRI, posterior femur registration marker sphere, segmentor is John Paul Smith (JPS), version 1, NifTI image
oks001_MRL-s_PTR-S_FXJ_03.nii:: oks001, sagittal ligament/tendon (connective tissue) MRI, superior patella registration marker sphere, segmentor is Fred Johnson (no middle name, FXJ), version 3, NifTI image
=== Geometry ===
TBD
=== Mesh ===
TBD
== Data Labeling ==
During data collection, the data sets, testing conditions, trials can be labeled through various conventions of experimentation systems and at the convenience of the personnel acquiring the data. Nonetheless, for data curation, organization, and dissemination data labels should be associated with
* specimen/sample label (see above), and
* an indicator/descriptor of experiment condition.
This information can be provided in
* the data label in an abbreviated form, or
* in the header of data files, or
* in a description file associated with the arbitrary data label.
== Data Curation ==
For a given whole knee specimen, Open Knee(s) data will be acquired asynchronously through a variety of modalities including anatomical imaging, mechanical testing of joints, and characterization of tissue specimens, see
* [[Specifications/ExperimentationAnatomicalImaging]]
* [[Specifications/ExperimentationJointMechanics]]
* [[Specifications/ExperimentationTissueMechanics]]
The in-house data management system, based on [[http://www.midasplatform.org/|Midas Platform]], will be used as a staging server for data curation and documentation. Once data is collected, the person leading the acquisition activity should ensure association of data labels, specimen/sample labels and provide descriptors of experiment conditions (see section above). In following, data should be uploaded to the in-house data management system for collation of different data sets and for organization. An example hierarchical structure for data organization is in following:
{{{
.
├── oks001
│ ├── joint
│ │ ├── patellofemoral
│ │ └── tibiofemoral
│ │ ├── photos
│ │ ├── readme.txt
│ │ └── trial001
│ ├── mri
│ │ ├── cartilage
│ │ ├── connective
│ │ │ ├── axial
│ │ │ ├── coronal
│ │ │ └── sagittal
│ │ └── general
│ ├── photos
│ ├── specs
│ └── tissue
│ ├── bone
│ ├── cartilage
│ ├── ligament
│ │ └── ACL
│ │ ├── photos
│ │ └── readme.txt
│ ├── meniscus
│ └── tendon
├── oks002
├── oks003
├── ...
}}}
== Data Dissemination ==
Once data for the whole knee is curated, organized and documented; the project website will be used for dissemination, through the "Downloads" section of https://simtk.org/home/openknee.
* For each specimen, there should be a download package, which may have different release versions based on the availability of data and models, see [[Roadmap]], e.g.
. Open Knee(s) Generation 2 - Specimen 1
* Different sections of specimen-specific data sets should be downloaded from the in-house data management site as individual files or compressed packages, e.g.
* oks001-mri.zip
* oks001-joint.zip
* oks001-tissue.zip
* Individual files or compressed files should be uploaded to the appropriate download package at the "Downloads" section of https://simtk.org/home/openknee.
* One should refer to individual specifications of each experimentation for details of relevant data dissemination procedure.
* An appropriate licensing should be selected, see [[Licensing]].
* The release version should be incremented based on the [[Roadmap]].