Changes between Version 21 and Version 22 of barSoftwareErrorCorrection


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Timestamp:
10/26/11 08:30:36 (13 years ago)
Author:
kubel
Comment:

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  • barSoftwareErrorCorrection

    v21 v22  
    77In 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.  
    88 
    9 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. 
    10  
    11 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. 
    12  
    13 Right: Histological slice visible through translucent final CAF slide. 
    14  
    15  
    16 [[Image(006__final_comparison.png)]] FIGURE 1 
     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. 
     10[[Image(006__final_comparison.png)]]  
    1711 
    1812---- 
    … …  
    5852the regular structures. 
    5953 
    60 Left: Red blocks mark regions where irregular neighboring lines touch each other creating small closed areas. 
    61  
    62 Middle: Small areas were detected by the parser, traced and marked as Unlabelled. 
    63  
    64 Right: Adjusting the threshold number of pixels that should be traces by parser excluded incorrectly recognized tiny structures. 
    65  
    66  
    67 [[Image(001__unlabelled_annotated.gif)]]FIGURE 2 
     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[[Image(001__unlabelled_annotated.gif)]] 
    6856 
    6957=== Incorrect label placement === 
    … …  
    7765Tracing 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. 
    7866 
    79  
    80 [[Image(003__invalid_labels_annotated.gif)]]FIGURE 3 
    81  
     67'''FIGURE 3.''' 
     68[[Image(003__invalid_labels_annotated.gif)]] 
    8269 
    8370=== Duplicated labels within a single contour === 
    … …  
    115102tremendous as compared with manual cleaning. 
    116103 
    117 Left: 
    118  
    119 Middle: 
    120  
    121 Right: 
    122  
    123 [[Image(002__gapfill_annotated.gif)]]FIGURE 4 
    124  
     104'''FIGURE 4.''' '''Left''':   '''Middle''':   '''Right''': 
     105[[Image(002__gapfill_annotated.gif)]] 
    125106---- 
    126107 
    … …  
    132113Unrecognized areas can be attributed to the structures from the upper hierarchy level.  
    133114 
    134 Left:  
    135 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). 
    136  
    137 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. 
    138  
    139 Right: Updated CAF slide. 
    140  
    141 [[Image(0041_new_edges_animated.gif)]]FIGURE 5 
    142  
     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. 
     116[[Image(0041_new_edges_animated.gif)]] 
    143117---- 
    144118=== Additional elements apart anatomical data included in CAF slide === 
    … …  
    146120In 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. 
    147121 
    148 Left:  
    149  
    150 Right: 
    151  
    152 [[Image(007__final_electrode.png)]]FIGURE 6 
    153  
     122'''FIGURE 6.''' 
     123[[Image(007__final_electrode.png)]] 
     124---- 
    154125== List of used abbreviations == 
    155126 
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