Changes between Version 11 and Version 12 of barSoftwareGapFillDetails
- Timestamp:
- 07/25/11 22:05:18 (13 years ago)
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barSoftwareGapFillDetails
v11 v12 1 1 = 3d Brain Atlas Reconstructor standalone = 2 2 3 [[PageOutline(2-3,,inline,unnumbered)]] 3 4 4 === Detailed description of gap-filling algorithm === 5 == Detailed description of gap-filling algorithm == 6 7 === Introduction === 5 8 6 9 The most common defect encountered in digital (e.g. PDF) versions of published atlases are gaps in structures' outlines. It commonly happens when two contour lines which should touch are drawn so that they leave a little space in between. Such an arrangement may not be visible in a printed atlas but it greatly disturbs tracing process where every pixel may influence the results. In this case the structure being traced overtakes the space of its neighbour through the broken contour which we call leaking of the structure (see figure below). … … 16 19 Consecutive flood-filled areas are dilated the same number of times as the boundaries were grown to make the area of the resulting path 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). 17 20 21 === Structures without gaps === 22 18 23 [[Image(debug_460_461_VO_step_0-anim-AOP.gif)]] 19 24 … … 27 32 || 5 || 51112 || 28 33 34 35 === Leaking strutcures === 29 36 30 37 [[Image(debug_460_461_VO_step_0-anim-VO.gif)]] … … 45 52 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. 46 53 47 === = Preconfiguration ====54 === Preconfiguration === 48 55 49 56 The gap filling algorithm may also be preconfigured during the preparation of a contour slide. Preconfiguration is carried out by assigning `bar:growlevel` … … 54 61 denote the number of dilation filter applications. 55 62 56 === = Algorithm efficacy and limitations ====63 === Algorithm efficacy and limitations === 57 64 58 65 Exemplary 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''.
