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MFSY committed Nov 10, 2020
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28 changes: 14 additions & 14 deletions docs/data-models/brainatlas/registering-brain-atlas.html
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Expand Up @@ -261,43 +261,43 @@ <h3><a href="#entities" name="entities" class="anchor"><span class="anchor-link"
</thead>
<tbody>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgsubjectcollection.html">SubjectCollection</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-subjectcollection.html">SubjectCollection</a> </td>
<td>A collection of subject to be used in the experiment </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgtemplateimagedata.html">TemplateImageData</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-templateimagedata.html">TemplateImageData</a> </td>
<td>Template image data acquired and processed from the subject collection </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgparcellationimagedata.html">ParcellationImageData</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-parcellationimagedata.html">ParcellationImageData</a> </td>
<td>Parcellation image data generated from the template image data </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgparcellationlabel.html">ParcellationLabel</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-parcellationlabel.html">ParcellationLabel</a> </td>
<td>Parcellation labels correspond to the annotations in the parcellation image </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgtemplatevolume.html">TemplateVolume</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-templatevolume.html">TemplateVolume</a> </td>
<td>Template volume generated from the template image data </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgparcellationvolume.html">ParcellationVolume</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-parcellationvolume.html">ParcellationVolume</a> </td>
<td>Parcellation volume generated from the parcellation image data </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgparcellationontology.html">ParcellationOntology</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-parcellationontology.html">ParcellationOntology</a> </td>
<td>Parcellation ontology converted from the parcellation label </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgatlasspatialreferencesystem.html">AtlasSpatialReferenceSystem</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-atlasspatialreferencesystem.html">AtlasSpatialReferenceSystem</a> </td>
<td>The spatial coordinate system of the atlas space </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgatlasrelease.html">AtlasRelease</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-atlasrelease.html">AtlasRelease</a> </td>
<td>An atlas release comprises template volume, parcellation volume, parcellation ontology as well as the atlas spatial reference system </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgexperimentalprotocol.html">Protocol</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-experimentalprotocol.html">Protocol</a> </td>
<td>Protocol that describes the method used in the design and execution of the experiment </td>
</tr>
</tbody>
Expand All @@ -312,19 +312,19 @@ <h3><a href="#activities" name="activities" class="anchor"><span class="anchor-l
</thead>
<tbody>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgatlasconstruction.html">Atlas Construction</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-atlasconstruction.html">Atlas Construction</a> </td>
<td>Process to construct a brain atlas </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgtemplatereconstruction.html">Template Reconstruction</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-templatereconstruction.html">Template Reconstruction</a> </td>
<td>Reconstruct the template image data into volumetric representation </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgparcellationreconstruction.html">Parcellation Reconstruction</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-parcellationreconstruction.html">Parcellation Reconstruction</a> </td>
<td>Reconstruct the parcellation image data into volumetric representation </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgontologyconversion.html">Ontology Conversion</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-ontologyconversion.html">Ontology Conversion</a> </td>
<td>Convert the parcellation label into ontological representation </td>
</tr>
</tbody>
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20 changes: 10 additions & 10 deletions docs/data-models/brainatlas/registering-whole-brain-morphology.html
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Expand Up @@ -258,31 +258,31 @@ <h3><a href="#entities" name="entities" class="anchor"><span class="anchor-link"
</thead>
<tbody>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgsubject.html">Subject</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-subject.html">Subject</a> </td>
<td>Subject that was used in the experiment </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgtemplatevolume.html">TemplateVolume</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-templatevolume.html">TemplateVolume</a> </td>
<td>Template volume generated from the template image data </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgatlasspatialreferencesystem.html">AtlasSpatialReferenceSystem</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-atlasspatialreferencesystem.html">AtlasSpatialReferenceSystem</a> </td>
<td>The spatial coordinate system of the atlas space </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgimagestack.html">ImageStack</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-imagestack.html">ImageStack</a> </td>
<td>Image stack obtained from the brain tissue of the subject </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgreconstructedcell.html">ReconstructedCell</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-reconstructedcell.html">ReconstructedCell</a> </td>
<td>Reconstructed cell </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgtransform.html">Transform</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-transform.html">Transform</a> </td>
<td>A linear or non-linear transform </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgexperimentalprotocol.html">Protocol</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-experimentalprotocol.html">Protocol</a> </td>
<td>Protocol that describes the method used in the design and execution of the experiment </td>
</tr>
</tbody>
Expand All @@ -297,15 +297,15 @@ <h3><a href="#activities" name="activities" class="anchor"><span class="anchor-l
</thead>
<tbody>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgbrainimaging.html">BrainImaging</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-brainimaging.html">BrainImaging</a> </td>
<td>Technique used to obtain an image stack of the brain tissue containing the cells for reconstruction </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgreconstructionfromimage.html">ReconstructionFromImage</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-reconstructionfromimage.html">ReconstructionFromImage</a> </td>
<td>Technique used to reconstruct the stained cell </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgtransformation.html">Transformation</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-transformation.html">Transformation</a> </td>
<td>Transform a geometric object </td>
</tr>
</tbody>
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Expand Up @@ -260,31 +260,31 @@ <h3><a href="#entities" name="entities" class="anchor"><span class="anchor-link"
</thead>
<tbody>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgsubject.html">Subject</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-subject.html">Subject</a> </td>
<td>Subject that was used in the experiment </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgslice.html">Slice</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-slice.html">Slice</a> </td>
<td>Brain slice obtained from the subject </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgintracellularsharpelectroderecordedslice.html">IntraCellularSharpElectrodeRecordedSlice</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-intracellularsharpelectroderecordedslice.html">IntraCellularSharpElectrodeRecordedSlice</a> </td>
<td>Brain slice containing recorded cells </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgintracellularsharpelectroderecordedslice.html">IntraSharpRecordedCellCollection</a></td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-intracellularsharpelectroderecordedslice.html">IntraSharpRecordedCellCollection</a></td>
<td>Collection of recorded cells in a single slice </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgintracellularsharpelectroderecordedcell.html">IntraCellularSharpElectrodeRecordedCell</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-intracellularsharpelectroderecordedcell.html">IntraCellularSharpElectrodeRecordedCell</a> </td>
<td>Cell that was recorded in the slice </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgtrace.html">Trace</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-trace.html">Trace</a> </td>
<td>Individual recording trace of the cell (stimulation/input and response/output trace) </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgexperimentalprotocol.html">Protocol</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-experimentalprotocol.html">Protocol</a> </td>
<td>Protocol that describes the method used in the design and execution of the experiment </td>
</tr>
</tbody>
Expand All @@ -300,15 +300,15 @@ <h3><a href="#activities" name="activities" class="anchor"><span class="anchor-l
</thead>
<tbody>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgbrainslicing.html">BrainSlicing</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-brainslicing.html">BrainSlicing</a> </td>
<td>Technique used to obtain a brain slice </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgintracellularsharpelectrode.html">IntraCellularSharpElectrode</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-intracellularsharpelectrode.html">IntraCellularSharpElectrode</a> </td>
<td>Technique used to study electrical activity of individual living cells </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgstimulusexperiment.html">StimulusExperiment</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-stimulusexperiment.html">StimulusExperiment</a> </td>
<td>Technique used to obtain the electrical signature of cells through injection of a defined current pattern </td>
</tr>
</tbody>
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Expand Up @@ -261,31 +261,31 @@ <h3><a href="#entities" name="entities" class="anchor"><span class="anchor-link"
</thead>
<tbody>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgsubject.html">Subject</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-subject.html">Subject</a> </td>
<td>Subject that was used in the experiment </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgslice.html">Slice</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-slice.html">Slice</a> </td>
<td>Brain slice obtained from the subject </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgpatchedslice.html">PatchedSlice</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-patchedslice.html">PatchedSlice</a> </td>
<td>Brain slice containing patched cells </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgpatchedcellcollection.html">PatchedCellCollection</a></td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-patchedcellcollection.html">PatchedCellCollection</a></td>
<td>Collection of patched cells in a single slice (e.g. for multi-patch recordings) </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgpatchedcell.html">PatchedCell</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-patchedcell.html">PatchedCell</a> </td>
<td>Cell that was patched in the slice </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgtrace.html">Trace</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-trace.html">Trace</a> </td>
<td>Individual recording trace of the patched cell (stimulation/input and response/output trace) </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgexperimentalprotocol.html">Protocol</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-experimentalprotocol.html">Protocol</a> </td>
<td>Protocol that describes the method used in the design and execution of the experiment </td>
</tr>
</tbody>
Expand All @@ -301,15 +301,15 @@ <h3><a href="#activities" name="activities" class="anchor"><span class="anchor-l
</thead>
<tbody>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgbrainslicing.html">BrainSlicing</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-brainslicing.html">BrainSlicing</a> </td>
<td>Technique used to obtain a brain slice for patching </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgwholecellpatchclamp.html">WholeCellPatchClamp</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-wholecellpatchclamp.html">WholeCellPatchClamp</a> </td>
<td>Technique used to study electrical activity of individual living cells </td>
</tr>
<tr>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-nsgstimulusexperiment.html">StimulusExperiment</a> </td>
<td><a href="https://bbp-nexus.epfl.ch/datamodels/class-stimulusexperiment.html">StimulusExperiment</a> </td>
<td>Technique used to obtain the electrical signature of cells through injection of a defined current pattern </td>
</tr>
</tbody>
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