Changes between Version 17 and Version 18 of barSoftwareGapFillDetails


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Timestamp:
08/22/11 18:13:47 (13 years ago)
Author:
danek
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  • barSoftwareGapFillDetails

    v17 v18  
    1010  '''Figure 1''': Examples of gaps in structures contours. 
    1111 
    12 Fragment of rasterized contor slide based on Paxinos and Franklin ''The Mouse Brain In Stereotaxic Coordinates, third edition''. 
     12Fragment of rasterized contour slide based on Paxinos and Franklin ''The Mouse Brain In Stereotaxic Coordinates, third edition''. 
    1313 
    14 Leaking structures are handled in 3dBAR by ''gap filling'' algorithm, an extension of the basic tracing procedure. 
    15 The main idea behind this algorithm is to expand the contours by applying [http://en.wikipedia.org/wiki/Dilation_%28morphology%29 dilation filter] filter until the boundary closes. 
     14Leaking structures are handled in 3dBAR by a ''gap filling'' algorithm, an extension of the basic tracing procedure. 
     15The main idea behind this algorithm is to expand the contours by applying [http://en.wikipedia.org/wiki/Dilation_%28morphology%29 dilation filter] until the boundary closes. 
    1616 
    17 The algorithm requires single input parameter – `MaxGrowLevel` describing maximal size of the gaps that may be closed during tracing of a particular area.  
    18  
    19 First, the initial bitmap is duplicated. Dilation filter is applied to the copy and the result is 
     17The algorithm requires a single input parameter – `MaxGrowLevel` - describing the maximum size of the gaps that may be closed during tracing of a particular area, and works as follows: First, the initial bitmap is duplicated. Dilation filter is applied to the copy and the result is 
    2018also cached. This procedure is repeated `MaxGrowLevel` times. Each application of the 
    2119dilation filter causes the boundaries of the structures to grow approximately 1 pixel in diameter. 
    … …  
    2422  [[Image(debug_460_461_VO_step_0-anim.gif)]] 
    2523 
    26   '''Figure 2''': Consecutive application of dilation filter to rasterized contour slide. 
     24  '''Figure 2''': Consecutive application of dilation filter to a rasterized contour slide. 
    2725 
    2826Structure areas on each cached bitmap are flood-filled and then dilated the same number of times as the boundaries were grown to ensure that the area of the resulting path stays unbiased. If it remains stable or slightly lowers (less than 2% in our implementation) at consecutive stages of the algorithm it means that most probably the boundaries of the structure in question do not have any gaps (see Fig. 3). 
    … …  
    4038 
    4139 
    42 If the reduction of flooded area at certain stage of filter application is grater than defined threshold (15-20% in our implementation), it means that boundary gap must have been closed (see Figure 4 below). After finding the optimal number of border expansions (denoted by `growlevel`) the corresponding bitmap is passed to [http://potrace.sourceforge.net/ PoTrace].  
     40If the reduction of flooded area at certain stage of filter application is greater than a defined threshold (15-20% in our implementation), it means that a gap in the boundary must have been closed (see Figure 4 below). After finding the optimal number of border expansions (denoted by `growlevel`) the corresponding bitmap is passed to [http://potrace.sourceforge.net/ PoTrace].  
    4341 
    4442  [[Image(debug_460_461_VO_step_0-anim-VO.gif)]] 
    … …  
    5654 
    5755 
    58 The gap filling algorithm is applied individually for each seed label thus different regions may be processed with different value of `growlevel`. Information about which `growlevel` was used to trace a particular path is stored in its attributes. 
     56The gap filling algorithm is applied individually for each seed label thus different regions may be processed with different values of `growlevel`. Information about which `growlevel` was used to trace a particular path is stored in its attributes. 
    5957 
    6058=== Preconfiguration === 
    … …  
    6967=== Algorithm efficacy and limitations === 
    7068 
    71 Table below summarizes result of the gap filling algorithm applied to 47 paths from 13th coronal section (2.1mm ant. from bregma) from Paxinos and Franklin ''The Mouse Brain In Stereotaxic Coordinates, third edition''. 
     69The table below summarizes results of the gap filling algorithm applied to 47 paths from 13th coronal section (2.1mm ant. from bregma) from Paxinos and Franklin ''The Mouse Brain In Stereotaxic Coordinates, third edition''. 
    7270 
    7371||= optimal grow level =||= number of paths =|| 
    … …  
    7674||  2       ||  10  || 
    7775 
    78 The performance of the algorithm depends on the initial size of the structure and on the bitmap resolution. Intensive use of this algorithm may distort or even erase some (particularly narrow) structures. There is no specific mechanism implemented against such behaviour. If a very accurate reconstruction is required, the best policy is to carefully prepare contour slides adjusting stroke width and slice resterization resolution so there is no need to apply gap filling. 
     76The performance of the algorithm depends on the initial size of the structure and on the bitmap resolution. Intensive use of this algorithm may distort or even erase some (particularly narrow) structures. There is no specific mechanism implemented against such behavior. If a very accurate reconstruction is required, the best policy is to carefully prepare contour slides adjusting stroke width and slice resterization resolution so there is no need to apply gap filling. 
    7977 
    8078{{{ 
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