PreProcessing.odml 25 KB

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  6. </style><body><header><h1><a class="white" href="https://templates.g-node.org/templates.xml">odML metadata document</a></h1></header><div class="navWrapper"><navigationContainer><div id="navigationContainer"><hr class="fatline" /><p><h2>Document info</h2><b>Author: </b><xsl:if test="author"><xsl:value-of select="author"/></xsl:if><br/><b>Date: </b><xsl:if test="date"><xsl:value-of select="date"/></xsl:if><br/><b>Version: </b><xsl:if test="version"><xsl:value-of select="version"/></xsl:if><br/><b>Repository: </b><xsl:if test="repository"><xsl:value-of select="repository"/></xsl:if><br/></p><hr class="fatline" /><h2>Structure</h2><font size ="-1" ><xsl:if test="section"><xsl:for-each select="section"><xsl:call-template name="sectionTemplate"><xsl:with-param name="navigation">1</xsl:with-param><xsl:with-param name="anchorBase">Sec</xsl:with-param><xsl:with-param name="url" select="$repository"/></xsl:call-template></xsl:for-each></xsl:if></font><br/></div><div id="contentContainer"><hr class="fatline" /><h2>Content</h2><xsl:if test="section"><xsl:for-each select="section"><xsl:call-template name="sectionTemplate"><xsl:with-param name="navigation">0</xsl:with-param><xsl:with-param name="anchorBase">Sec</xsl:with-param><xsl:with-param name="url" select="$repository"/></xsl:call-template></xsl:for-each></xsl:if></div></navigationContainer></div></body></html></xsl:template><xsl:template name="sectionTemplate" match="section"><xsl:param name="navigation"/><xsl:param name="anchorBase"/><xsl:param name="url"/><xsl:variable name="anchorName" select="concat($anchorBase,position())"/><xsl:variable name="repository"><xsl:choose><xsl:when test="repository"><xsl:value-of select ="repository"/></xsl:when><xsl:otherwise><xsl:value-of select ="$url"/></xsl:otherwise></xsl:choose></xsl:variable><xsl:choose><xsl:when test="$navigation = 1"><ol class="nested"><font size="normal"><a href="#{$anchorName}"><xsl:value-of select="name"/> (type: <xsl:value-of select="type"/>)</a></font><xsl:if test="section"><xsl:for-each select="section"><xsl:call-template name="sectionTemplate"><xsl:with-param name="navigation" select="$navigation"/><xsl:with-param name="anchorBase" select="concat($anchorName,'SubSec')"/><xsl:with-param name="url" select="$repository"/></xsl:call-template></xsl:for-each></xsl:if></ol></xsl:when><xsl:otherwise><a name="{$anchorName}"><h3><xsl:value-of select="name"/> Section</h3></a><p><b>Type: </b><xsl:value-of select="type"/><br/><xsl:choose><xsl:when test ="repository"><b>Repository: </b><xsl:value-of select="repository"/><br/></xsl:when><xsl:otherwise><b>Repository: </b><xsl:value-of select="$repository"/><br/></xsl:otherwise></xsl:choose><b>Link: </b><xsl:if test="link"><xsl:value-of select="link"/></xsl:if><br/><b>Include:</b><xsl:if test="include"><font color="red"><xsl:value-of select="include"/></font></xsl:if><br/><b>Definition: </b><xsl:if test="definition"><xsl:value-of select="definition"/></xsl:if><br/></p><xsl:if test="property"><table border="1" rules="rows" width="100%"><font size="-1"><tr bgcolor="#336699" align="left" valign="middle"><th><font size="+1" color="white"><b>Name</b></font></th><th><font size="+1" color="white"><b>Value</b></font></th><th><font size="+1" color="white"><b>Unit</b></font></th><th><font size="+1" color="white"><b>Type</b></font></th><th><font size="+1" color="white"><b>Uncertainty</b></font></th><th><font size="+1" color="white"><b>Definition</b></font></th><th><font size="+1" color="white"><b>Dependency</b></font></th><th><font size="+1" color="white"><b>Dependency Value</b></font></th></tr><xsl:for-each select="property"><xsl:variable name="anchor"><xsl:value-of select ="name"/></xsl:variable><tr><td width="15%"><a name="{$anchor}"/><p><xsl:value-of select="name"/></p></td><td width="10%"><p><xsl:value-of select="value"/></p></td><td width="5%"><p><xsl:value-of select="unit"/><br/></p></td><td width="5%"><p><xsl:value-of select="type"/></p></td><td width="5%"><p><xsl:value-of select="uncertainty"/><br/></p></td><td width="22.5%"><p><xsl:value-of select="definition"/></p></td><td width="5%"><p><xsl:value-of select="dependency"/></p></td><td width="5%"><p><xsl:value-of select="dependencyValue"/></p></td></tr></xsl:for-each></font></table></xsl:if><a href="#top"><tiny>top</tiny></a><hr class="thinline" /><xsl:if test="section"><xsl:for-each select="section"><xsl:call-template name="sectionTemplate"><xsl:with-param name="navigation" select="$navigation"/><xsl:with-param name="anchorBase" select="concat($anchorName,'SubSec')"/><xsl:with-param name="url" select="$repository"/></xsl:call-template></xsl:for-each></xsl:if></xsl:otherwise></xsl:choose></xsl:template>
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  8. <id>060511ec-fec0-4406-8bc6-9f26ece6db52</id>
  9. <section>
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  11. <type>preprocessing</type>
  12. <name>PreProcessing</name>
  13. <definition>Information on preprocessing performed on the data, e.g., rejections of trial and electrodes, spike sorting.</definition>
  14. <section>
  15. <id>8a929183-6578-43ed-8517-7ee0ab197b5b</id>
  16. <type>subject/preparation</type>
  17. <name>HFC</name>
  18. <definition>Information on rejected trials and rejected electrodes based on LFPs filtered in the HFC band</definition>
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  20. <id>9d7e799d-7073-4179-9b09-a8236162cf3b</id>
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  22. <value>250.0</value>
  23. <unit>Hz</unit>
  24. <definition>High cut frequency of rejection filter</definition>
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  32. <unit>Hz</unit>
  33. <definition>Low cut frequency of rejection filter</definition>
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  49. <definition>ID list of rejected electrodes</definition>
  50. <type>int</type>
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  57. <definition>ID list of rejected trials</definition>
  58. <type>int</type>
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  61. </section>
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  63. <id>ad179d2e-3f83-4d82-880b-284d60949965</id>
  64. <type>subject/preparation</type>
  65. <name>LFC</name>
  66. <definition>Information on rejected trials and rejected electrodes based on LFPs filtered in the LFC band</definition>
  67. <property>
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  87. <name>Order</name>
  88. <value>2</value>
  89. <definition>Order of rejection filter</definition>
  90. <type>int</type>
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  93. <property>
  94. <id>ef328feb-bd2e-411b-9e9c-e8f3c2dc0084</id>
  95. <name>RejElectrodes</name>
  96. <value>[15,23,38,45,46,53,67]</value>
  97. <definition>ID list of rejected electrodes</definition>
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  105. <definition>ID list of rejected trials</definition>
  106. <type>int</type>
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  109. </section>
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  112. <type>subject/preparation</type>
  113. <name>IFC</name>
  114. <definition>Information on rejected trials and rejected electrodes based on LFPs filtered in the IFC band</definition>
  115. <property>
  116. <id>796e43a1-9a73-4a45-ac30-94c8ba324bca</id>
  117. <name>Highcut</name>
  118. <value>40.0</value>
  119. <unit>Hz</unit>
  120. <definition>High cut frequency of rejection filter</definition>
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  142. <id>6e050698-90e4-4318-af17-3de85a583ae6</id>
  143. <name>RejElectrodes</name>
  144. <value>[23,45]</value>
  145. <definition>ID list of rejected electrodes</definition>
  146. <type>int</type>
  147. <value_origin>i140703-001_rej_012Hz-040Hz-03o.hdf5</value_origin>
  148. </property>
  149. <property>
  150. <id>3137ccd2-b6f5-45ab-b318-744dbfce362c</id>
  151. <name>RejTrials</name>
  152. <value>[146,1,126,139,23,46,47,4,10,74,75,89,157,158,93,19,127,84,87,124]</value>
  153. <definition>ID list of rejected trials</definition>
  154. <type>int</type>
  155. <value_origin>i140703-001_rej_012Hz-040Hz-03o.hdf5</value_origin>
  156. </property>
  157. </section>
  158. <section>
  159. <id>3fc46e54-a650-44e3-807a-ce4edcb3e036</id>
  160. <type>subject/preparation</type>
  161. <name>OfflineSpikeSorting</name>
  162. <definition>Information on spike sorting</definition>
  163. <section>
  164. <id>ea5231d5-d55b-4bd2-aba4-11797cfbd15a</id>
  165. <type>subject/preparation</type>
  166. <name>Sorting-03</name>
  167. <definition>Information on one particular spike sorting of the data</definition>
  168. <property>
  169. <id>30d5ae40-143d-4c36-a28d-d70f87af3193</id>
  170. <name>Filename</name>
  171. <value>I140703-001-03</value>
  172. <definition>File containing results of offline spike sorting</definition>
  173. <type>string</type>
  174. </property>
  175. <property>
  176. <id>86bbcc8f-835b-4ec0-9da3-7d4e3cc21947</id>
  177. <name>Method</name>
  178. <value>[K-Means,Valley-Seeking]</value>
  179. <definition>Clustering method(s) used for sorting</definition>
  180. <type>string</type>
  181. </property>
  182. <property>
  183. <id>58f4d28e-2747-45f8-a0fe-705e259f9879</id>
  184. <name>MethodType</name>
  185. <value>semi-automatic</value>
  186. <definition>Level of supervision of the method (manual/semi-automatic/automatic)</definition>
  187. <type>string</type>
  188. </property>
  189. <property>
  190. <id>c3a51e43-3d48-4338-8f5e-209118957c91</id>
  191. <name>OutlierThreshold</name>
  192. <value>[1.8,2.0]</value>
  193. <definition>Threshold used to remove outliers from the unit clusters</definition>
  194. <type>float</type>
  195. </property>
  196. <property>
  197. <id>4c2cc518-6ebe-49ec-b405-0d8d29dcde14</id>
  198. <name>TotalNum_SUAs</name>
  199. <value>156</value>
  200. <definition>Total number of offline sorted SUA units</definition>
  201. <type>int</type>
  202. </property>
  203. <property>
  204. <id>44427748-7f01-470b-a6a9-323687e48427</id>
  205. <name>TotalNum_MUAs</name>
  206. <value>19</value>
  207. <definition>Total number of offline sorted MUA units</definition>
  208. <type>int</type>
  209. </property>
  210. <property>
  211. <id>03b6406c-5fa5-410a-9480-8c089167cd94</id>
  212. <name>NoiseUnitIDs</name>
  213. <value>[0,255]</value>
  214. <definition>Unit ID(s) reserved for noise in the offline spike sorting</definition>
  215. <type>int</type>
  216. </property>
  217. <property>
  218. <id>65bb1071-ed54-466c-80b6-450c3b7a653e</id>
  219. <name>SyncChannelLimit</name>
  220. <value>70</value>
  221. <definition>Minimum percentage of channels with a synchronously detected spike events used to reject these spike events</definition>
  222. <type>int</type>
  223. </property>
  224. </section>
  225. <property>
  226. <id>330e5be6-690a-4e48-8752-2ce7ac9ea124</id>
  227. <name>Software</name>
  228. <value>Plexon Offline Spike Sorter</value>
  229. <definition>Software used to perform offline spike sorting</definition>
  230. <type>string</type>
  231. </property>
  232. <property>
  233. <id>51a38582-2487-4977-bae0-f481b778b86f</id>
  234. <name>SoftwareVersion</name>
  235. <value>3.3</value>
  236. <definition>Software version used to perform offline spike sorting</definition>
  237. <type>string</type>
  238. </property>
  239. <property>
  240. <id>5b7ee2e0-6b79-4946-871b-b9aba376227b</id>
  241. <name>ResponsiblePerson</name>
  242. <value>Alexa Riehle</value>
  243. <definition>Name of the person who performed the sorting</definition>
  244. <type>string</type>
  245. </property>
  246. <property>
  247. <id>f5dd155b-7be4-45a0-acb5-0b8078e90e0a</id>
  248. <name>Sortings</name>
  249. <value>-03</value>
  250. <definition>IDs of sorting versions available for this dataset</definition>
  251. <type>string</type>
  252. </property>
  253. </section>
  254. <property>
  255. <id>c19308f0-9ed1-4cd8-b6c9-e423a75026b3</id>
  256. <name>LFPBands</name>
  257. <value>[HFC,LFC,IFC]</value>
  258. <definition>List of identifiers of different frequency bands for which an analysis to determine trials and electrodes to be rejected were performed.</definition>
  259. <type>string</type>
  260. </property>
  261. </section>
  262. </odML>