Changes between Version 22 and Version 23 of barSoftwareErrorCorrection
- Timestamp:
- 10/26/11 08:33:15 (13 years ago)
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barSoftwareErrorCorrection
v22 v23 7 7 In our work-flow we introduced a stage of ''contour slides'' - vector graphic in SVG format (for detailed description see Majka et al 2011) that simplifies necessary corrections, manual preparation of structures' outlines from histology results and further improvements of slide details. 8 8 9 '''FIGURE 1.''' '''Left''': Coronal slice of a rat brain around 3 mm behind Bregma stained for Cytochrome Oxidase. Histological verification of the electrodes' location after chronic local field potentials (LFP) recording from the thalamic somatosensory nuclei. '''Middle''': Initial stage of manual preparation of a ''countour slide''. Main structures outlines drawn over the histology slice (line thickness increased for better visibility) and structure labels placed over well recognized regions. '''Right''': Histological slice visible through translucent final CAF slide. 9 '''FIGURE 1.''' [[BR]] 10 '''Left''': Coronal slice of a rat brain around 3 mm behind Bregma stained for Cytochrome Oxidase. Histological verification of the electrodes' location after chronic local field potentials (LFP) recording from the thalamic somatosensory nuclei. '''Middle''': Initial stage of manual preparation of a ''countour slide''. Main structures outlines drawn over the histology slice (line thickness increased for better visibility) and structure labels placed over well recognized regions. '''Right''': Histological slice visible through translucent final CAF slide. 10 11 [[Image(006__final_comparison.png)]] 11 12 … … 52 53 the regular structures. 53 54 54 '''FIGURE 2.''' '''Left''': Red blocks mark regions where irregular neighboring lines touch each other creating small closed areas. '''Middle''': Small areas were detected by the parser, traced and marked as Unlabelled. '''Right''': Adjusting the threshold number of pixels that should be traces by parser excluded incorrectly recognized tiny structures. 55 '''FIGURE 2.''' [[BR]] 56 '''Left''': Red blocks mark regions where irregular neighboring lines touch each other creating small closed areas. '''Middle''': Small areas were detected by the parser, traced and marked as Unlabelled. '''Right''': Adjusting the threshold number of pixels that should be traces by parser excluded incorrectly recognized tiny structures. 55 57 [[Image(001__unlabelled_annotated.gif)]] 56 58 … … 65 67 Tracing of a region corresponding to the incorrectly placed label is skipped but in general tracing is not interrupted as the whole procedure works non-interactively. 66 68 67 '''FIGURE 3.''' 69 '''FIGURE 3.''' [[BR]] 68 70 [[Image(003__invalid_labels_annotated.gif)]] 69 71 … … 102 104 tremendous as compared with manual cleaning. 103 105 104 '''FIGURE 4.''' '''Left''': '''Middle''': '''Right''':106 '''FIGURE 4.'''[[BR]] 105 107 [[Image(002__gapfill_annotated.gif)]] 106 108 ---- … … 113 115 Unrecognized areas can be attributed to the structures from the upper hierarchy level. 114 116 115 '''FIGURE 5.''' '''Left''': Blinking lines and appropriate labels were added to the ''contour slide'' 1) to show primary somatosensory representation of big facial whiskers ("barrel field", S1BF) in the cerebral cortex (Cx); 2) to separate ventral posteromedial (VPM) and ventral posterolateral (VPL) nuclei from ventrobasal complex (VB). Unrecognized thalamic nuclei, which were not labeled with their specific names, are labeled with "Th" so they all will be included in the final reconstruction of the thalamus. '''Right''': Updated CAF slide. 117 '''FIGURE 5.'''[[BR]] 118 '''Left''': Blinking lines and appropriate labels were added to the ''contour slide'' 1) to show primary somatosensory representation of big facial whiskers ("barrel field", S1BF) in the cerebral cortex (Cx); 2) to separate ventral posteromedial (VPM) and ventral posterolateral (VPL) nuclei from ventrobasal complex (VB). Unrecognized thalamic nuclei, which were not labeled with their specific names, are labeled with "Th" so they all will be included in the final reconstruction of the thalamus. '''Right''': Updated CAF slide. 116 119 [[Image(0041_new_edges_animated.gif)]] 117 120 ---- … … 120 123 In our example we include in the slide an outline of the electrode. Spaces occupied by lesions or injected dyes can be added to brain elements. 121 124 122 '''FIGURE 6.''' 125 '''FIGURE 6.'''[[BR]] 123 126 [[Image(007__final_electrode.png)]] 124 127 ----
