001 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 002 003 SETTINGS FILE FOR ROXAS-BASED ANALYISIS OF XYLEM ANATOMY 004 005 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 006 007 GENERAL 008 Pinus leucodermis_0.833 <- Configuration 009 31.03.2016 23:59:36 <- File created 010 3.0.0 <- ROXAS version 011 vonarx <- Author 012 <- Comment 013 014 015 -------------------------------------------------------------------------------------- 016 MAIN WINDOW 017 1 <- Linear core (Y) / circular sample (N) 018 179 <- Lower Limit [°] 019 181 <- Upper Limit [°] 020 2016 <- Outmost Year 021 1 <- Only global xylem analysis 022 0 <- Manually select AOI's 023 0 <- Consider outline trace in analysis 024 0 <- Extended visual output 025 0 <- Parenchyma analysis 026 1 <- Cell lumen area & CWT (as opposed to lumen area only) 027 0 <- Manually select AOE's 028 029 -------------------------------------------------------------------------------------- 030 CELL EXTRACTION 031 5 <- Area low threshold 032 100 <- Area mid threshold 033 2000 <- Area up threshold 034 0 <- Roundness weight 035 7 <- Roundness low threshold 036 3.5 <- Roundness mid threshold 037 2.5 <- Roundness up threshold 038 0 <- Perimeter Ratio weight 039 0.97 <- Perimeter Ratio low threshold 040 0.95 <- Perimeter Ratio mid threshold 041 0.95 <- Perimeter Ratio up threshold 042 0 <- Area/Box weight 043 0.75 <- Area/Box low threshold at Area low threshold 044 0.6 <- Area/Box mid threshold at Area low threshold 045 0.5 <- Area/Box up threshold at Area low threshold 046 1 <- Area/Box low threshold at Area up threshold 047 1 <- Area/Box mid threshold at Area up threshold 048 0.9 <- Area/Box up threshold at Area up threshold 049 0 <- Aspect weight 050 15 <- Aspect low threshold 051 6 <- Aspect mid threshold 052 2 <- Aspect up threshold 053 0 <- Caliper-Diameter Ratio weight 054 1.3 <- Caliper-Diameter Ratio low threshold 055 1.2 <- Caliper-Diameter Ratio mid threshold 056 1.1 <- Caliper-Diameter Ratio up threshold 057 0 <- Fractal Dimension weight 058 1 <- Fractal Dimension low threshold 059 1.08 <- Fractal Dimension mid threshold 060 1.12 <- Fractal Dimension up threshold 061 062 063 064 065 066 -------------------------------------------------------------------------------------- 067 EARLYWOOD EXTRACTION 068 2 <- Relative cell size: N° of cells to compare with 069 40 <- Relative cell size: Maximal tangential distance 070 20 <- Relative cell size: Maximal radial distance 071 5 <- Relative cell size: Radial distance margin 072 2 <- Radial Heterogeneity: N° of cells to compare with 073 40 <- Radial Heterogeneity: Maximal tangential distance 074 20 <- Radial Heterogeneity: Maximal radial distance 075 5 <- Radial Heterogeneity: Radial distance margin 076 2 <- Tangential Density: N° of cells to compare with 077 400 <- Tangential Density: Maximal tangential distance 078 150 <- Tangential Density: Maximal radial distance 079 1 <- Absolute Size: weight 080 400 <- Absolute Size: threshold value 081 1 <- Relative Size: weight 082 140 <- Relative Size: threshold value 083 1 <- Heterogeneity: weight 084 140 <- Heterogeneity: threshold value 085 0 <- Distance Density: weight 086 5 <- Distance Density: threshold value 087 0 <- Area Density: weight 088 80 <- Area Density: threshold value 089 090 091 092 093 -------------------------------------------------------------------------------------- 094 EARLYWOOD BORDER EXTRACTION 095 0 <- Minimal N° of cells in neighbourhood window 096 20 <- Maximal tangential distance 097 50 <- Maximal radial distance 098 10 <- Radial distance margin 099 105 <- Threshold Level for Earlywood Border 100 1 <- Apply Earlywood border cleaning 101 120 <- Macro-Cleaning: Maximal tangential distance 102 40 <- Macro-Cleaning: Maximal radial distance 103 5 <- Macro-Cleaning: Critical N° of Earlywood border cells in neighbourhood window 104 10 <- Micro-Cleaning: Maximal tangential distance 105 17.5 <- Micro-Cleaning: Maximal radial distance 106 0 <- Micro-Cleaning: Critical N° of Earlywood border cells in neighbourhood window 107 108 109 110 111 -------------------------------------------------------------------------------------- 112 ANNUAL RING DETERMINATION 113 30 <- Aperture of catcher minimum 114 100 <- Aperture of catcher maximum 115 0.5 <- Catcher maximum at angular distance 116 400 <- Maximal change of retrival vector [units of measurements / degree] 117 1 <- Minimal angle difference for retrieval vector calculation 118 0.02 <- Vertex spacing of ring borders in [°] 119 1 <- Apply global ring property cleaning 120 80 <- Minimal proportion of ring angle extent in relation to entire sector 121 0.04 <- At least 1 border cell every ... degrees 122 123 124 125 126 -------------------------------------------------------------------------------------- 127 IMAGE PROCESSING 128 0.1 <- Red 129 0.55 <- Green 130 0.45 <- Blue 131 1 <- Use large spectral filter 132 0 <- Dark cell lumen 133 100 <- Strength of contrast homogenization 134 5 <- Lower limit [%] 135 95 <- Upper limit [%] 136 1 <- Perform Diff. of Gaussians 137 3 <- Small Gauss kernel 138 11 <- Large Gauss kernel 139 3 <- Erosion Kernel 140 0 <- Perform simple enhancement 141 0 <- Blind out intensity 142 1 <- Scale up factor 143 1 <- Reduce noise 144 100 <- Lower limit [0-255] 145 255 <- Upper limit [0-255] 146 147 148 149 150 -------------------------------------------------------------------------------------- 151 CELL ANALYSIS 152 1 <- Use sub-images for cell extraction 153 15 <- Height of sub-images: (1'000'000 / width) x ... 154 1.3 <- Overlap of sub-images (widest cell diam.) x ... 155 0 <- Auto-Split 156 1 <- Watershed-Split 157 2 <- N° of Erosions 158 1 <- Additional final cell split 159 1 <- Restricted Dilation 160 150 <- Lower Segmnt. limit 161 3 <- N° of iterations 162 0 <- Cell outline Smoothing 163 1 <- Strength 164 0 <- Convex cell outline 165 0 <- Eliminate cells touching AOI border 166 0 <- Double cell wall thickness [µm] 167 2 <- Window size (widest cell diam.) x ... 168 50 <- Threshold group size 169 0 <- Don't fill holes during cell extraction 170 0 <- No Cell Splitting 171 1 <- Remove protrusions 172 2 <- Sensitivity [µm] of removing protrusions 173 -------------------------------------------------------------------------------------- 174 PARENCHYMA RAY ANALYSIS 175 0 <- Analyze parenchyma rays 176 0.2 <- Angular resolution 177 2 <- Small-scale: N° Runs 178 5 <- Small-scale: Range 179 0.4 <- Small-scale: Threshold 180 1 <- Large-scale: N° Runs 181 19 <- Large-scale: Range 182 0.5 <- Large-scale: Threshold 183 184 185 186 187 -------------------------------------------------------------------------------------- 188 MISCELLANEOUS 189 40 <- Font size of calendar year labels [µm] 190 1 <- Life screen update 191 0 <- Run ROXAS in debugging mode 192 <- Outmost (peripheral) ring border was drawn 193 3 <- Color of cell outlines: 0 - red, 1 - yellow, 2 - green, 3 - cyan, 4 - blue, 5 - magenta 194 1 <- Save ROXAS data also as text files 195 1 <- Visualize cell wall thickness measurements with circles 196 200 <- N° of cells for which to visualize cell wall thickness 197 1 <- Color of ring borders & labels: 0 - red, 1 - yellow, 2 - green, 3 - cyan, 4 - blue, 5 - magenta, 6 - white, 7 - black 198 2 <- Color of AOE's, AOI's & Xylem outlines: 0 - red, 1 - yellow, 2 - green, 3 - cyan, 4 - blue, 5 - magenta, 6 - white, 7 - black 199 0 <- Classify AOEs and calculate % area of poor sample quality AOEs for ring deciles 200 201 -------------------------------------------------------------------------------------- 202 CONIFERS 203 8 <- Maximum radial cell wall thickness of smallest tracheids [µm] 204 6 <- Maximum radial cell wall thickness of largest tracheids [µm] 205 0.75 <- Width of CWT retrieval window in proportion to tracheid width/height 206 1.5 <- Quality control: maximum relation of two opposing CWT 207 8 <- Maximum tangential cell wall thickness of smallest tracheids [µm] 208 6 <- Maximum tangential cell wall thickness of largest tracheids [µm] 209 210 211 212 213 -------------------------------------------------------------------------------------- 214 COLOR FILTERING 215 0 <- Lower limit of overall mean color intensity 216 0 <- Lower limit of red color channel intensity 217 0 <- Lower limit of green color channel intensity 218 0 <- Lower limit of blue color channel intensity 219 255 <- Upper limit of overall mean color intensity 220 255 <- Upper limit of red color channel intensity 221 255 <- Upper limit of green color channel intensity 222 255 <- Upper limit of blue color channel intensity 223 5 <- Lower cell area limit for intensity filtering 224 1000 <- Upper cell area limit for intensity filtering 225 226 227 228 -------------------------------------------------------------------------------------- 229 NEEDLE ANALYSIS 230 0 <- Analyze needles 231 1 <- Kernel size of Closing filter (Erode-Dilate) to remove noise 232 1 <- Needle length calculation: (perimeter - x times width) / 2 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250