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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), 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: 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:
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  3. Tissue Sample/data labels: The tissue location is labeled starting from its gross location and ending with its granular position.
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'''Note:''' Trial number will appear only for data files.  * 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
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Examples (only tissue type and tissue location are shown):
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Labeling convention: specimen identifier - tissue type identifier - location identifier (1 character for each direction. e.g MA= medial anterior) - trial number/ sample number identifier

 * Cartilage:
  * OK_ _-FMC-MXXX-_ _ (medial femoral cartilage)
  * OK_ _-FMC-LXXX-_ _ (lateral femoral cartilage)
  * OK_ _-FMC-AXXX-_ _ (Trochlear groove)
  * OK_ _-PTC-MXXX-_ _ (Patellar cartilage)
  * OK_ _-TBC-MXXX-_ _(medial tibial cartilage)
  * OK_ _-TBC-LXXX-_ _(lateral tibial cartilage)


'''Note:''' Depth identifiers: u = superficial layer, v=middle layer, w=deep layer

 * Meniscus:
  * OK_ _-MNS-(MAXX/MPXX/MCXX)-_ _ (Location identifiers : A (anterior), P (posterior), C (center))
  * OK_ _-MNS-(LAXX/LPXX/LCXX)-_ _


 * Tendon:
  * OK_ _-QAT-(SXXX/CXXX/IXXX)-_ _ (Location identifiers : S (Superior), C (center/ mid-substance), I (Inferior))

 * Ligaments:
  * OK_ _-ACL-(SXXX/CXXX/IXXX)-_ _ (Location identifiers : S (Superior), C (center/mid-substance), I (Inferior))
  * OK_ _-PCL-(SXXX/CXXX/IXXX)-_ _
  * OK_ _-MCL-(SXXX/CXXX/IXXX)-_ _
  * OK_ _-LCL-(SXXX/CXXX/IXXX)-_ _
  * OK_ _-PTL-(SXXX/CXXX/IXXX)-_ _		  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
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 attachment:tissue_label.txt
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'''Note:''' Trial number will appear only for data files.

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

Previous Protocols

  • ["Specifications/Specimens"]
  • ["Specifications/SpecimenPreparation"]

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

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

Data Labeling

  • Online storage of annotated data for prospective
    • discoverability (for internal use)
    • retrieval (for internal use),
    • and dissemination (through Open Knee(s) site at SimTK.org)

Data Curation

Note: Trial number will appear only for data files.

Data Dissemination

Specifications/DataManagement (last edited 2019-04-05 18:29:59 by owings)