source: proteomics, 2003, vol.3, pp.392-401 authors: paul cutler, geoffrey heald, ian r
DESCRIPTION
A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection. Source: Proteomics, 2003, vol.3, pp.392-401 Authors: Paul Cutler, Geoffrey Heald, Ian R. White and Jason Ruan Speaker: Shu-Fen Chiou ( 邱淑芬 ) Date: 2005/03/18. - PowerPoint PPT PresentationTRANSCRIPT
1
A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection
Source: Proteomics, 2003, vol.3, pp.392-401
Authors: Paul Cutler, Geoffrey Heald, Ian R.
White and Jason Ruan
Speaker: Shu-Fen Chiou (邱淑芬 )
Date: 2005/03/18
2
Outline
Introduction Proposed Method Experimental results Conclusions Comment
3
Introduction
A common goal of proteomic analysis:Quantitation and identification of proteins which are
differentially expressed under defined physiological
conditions. 2D-gel is a proteomic technology.
4
Introduction
Drawbacks of the available methods: Noise and artefacts Need extensive parameter setting Take much time Operator subjectivity
A new method using a segmentation method involving pixel value collection via serial analysis of the image through its range of density levels.
5
Proposed method
1616 2d gel image
244 239 233 230 232 236 241 240 242 243 243 243 244 246 244 244
234 218 201 185 190 208 230 237 240 241 242 245 244 244 244 242
228 201 176 157 161 186 221 234 240 242 242 244 244 244 242 243
224 189 157 132 141 174 214 229 237 242 240 242 244 244 243 243
233 212 188 168 177 203 228 235 239 240 239 241 242 243 244 244
239 227 213 202 208 221 234 238 239 237 236 239 241 243 244 243
242 238 236 235 235 236 238 238 232 217 209 212 223 235 243 243
231 241 240 239 239 239 237 234 213 179 162 166 190 217 239 242
229 239 240 240 240 238 233 222 175 123 105 109 135 182 227 239
239 238 240 239 241 240 229 206 132 75 61 67 87 146 214 234
239 238 239 239 241 241 229 200 120 67 56 61 79 139 213 234
239 239 237 238 240 241 231 208 135 80 67 73 97 157 221 236
241 240 238 240 241 241 235 222 174 124 109 118 148 193 231 240
240 240 240 240 241 241 238 228 194 157 144 155 180 212 235 239
240 240 239 240 243 243 239 233 217 200 196 204 217 231 239 240
236 235 238 239 241 242 240 237 229 223 221 227 235 237 236 234
Smallest pixel value:246
Highest pixel value:56
Limits:
•Size (maxSize, minSize)
•Shape (ellipse or circle)
6
Proposed method0
10
20
30
40
50
60
70
80
90
100
110
120
130
140
150
160
170
180
190
200
210
220
230
240
250
260
1 9 17 25 33 41 49 57 65 73 81 89 97 105113121129137 145153161169177185193201209217225 233241249High
Low
Range:20
675661The first range:56~76
Threshold 1: (56+61+67)/3=61
105109
The second range:105~125Threshold 2: (105+109)/2=107
7
Proposed method
244
239
233
230
232
236
241
240
242
243
243
243
244
246
244
244
234
218
201
185
190
208
230
237
240
241
242
245
244
244
244
242
228
201
176
157
161
186
221
234
240
242
242
244
244
244
242
243
224
189
157
132
141
174
214
229
237
242
240
242
244
244
243
243
233
212
188
168
177
203
228
235
239
240
239
241
242
243
244
244
239
227
213
202
208
221
234
238
239
237
236
239
241
243
244
243
242
238
236
235
235
236
238
238
232
217
209
212
223
235
243
243
231
241
240
239
239
239
237
234
213
179
162
166
190
217
239
242
229
239
240
240
240
238
233
222
175
123
105
109
135
182
227
239
239
238
240
239
241
240
229
206
132
75 61 67 87146
214
234
239
238
239
239
241
241
229
200
120
67 56 61 79139
213
234
239
239
237
238
240
241
231
208
135
80 67 73 97157
221
236
241
240
238
240
241
241
235
222
174
124
109
118
148
193
231
240
240
240
240
240
241
241
238
228
194
157
144
155
180
212
235
239
240
240
239
240
243
243
239
233
217
200
196
204
217
231
239
240
236
235
238
239
241
242
240
237
229
223
221
227
235
237
236
234
Threshold 1:61
Find the pixel <= threshold 1
1
1 1
minSize:12
maxSize:28Spot 1: (10,9), (10,10), (11,10)
8
Proposed method
244
239
233
230
232
236
241
240
242
243
243
243
244
246
244
244
234
218
201
185
190
208
230
237
240
241
242
245
244
244
244
242
228
201
176
157
161
186
221
234
240
242
242
244
244
244
242
243
224
189
157
132
141
174
214
229
237
242
240
242
244
244
243
243
233
212
188
168
177
203
228
235
239
240
239
241
242
243
244
244
239
227
213
202
208
221
234
238
239
237
236
239
241
243
244
243
242
238
236
235
235
236
238
238
232
217
209
212
223
235
243
243
231
241
240
239
239
239
237
234
213
179
162
166
190
217
239
242
229
239
240
240
240
238
233
222
175
123
105
109
135
182
227
239
239
238
240
239
241
240
229
206
132
75 61 67 87146
214
234
239
238
239
239
241
241
229
200
120
67 56 61 79139
213
234
239
239
237
238
240
241
231
208
135
80 67 73 97157
221
236
241
240
238
240
241
241
235
222
174
124
109
118
148
193
231
240
240
240
240
240
241
241
238
228
194
157
144
155
180
212
235
239
240
240
239
240
243
243
239
233
217
200
196
204
217
231
239
240
236
235
238
239
241
242
240
237
229
223
221
227
235
237
236
234
Threshold 2:107
Find the pixel <= threshold 2
1
1 1 1
1 1
1 1 1 1
minSize:12
maxSize:28Spot 1: (10,9), (10,10), (11,10), (9,9), …
9
Experimental results
10
Experimental results
11
Experimental results
12
Experimental results
13
Experimental results
14
Compare with edge detection
Edge detection Proposed method
15
Conclusions
The method can be automated and hence reduce operator subjectivity.
The method can detect a large dynamic range of spot intensities and areas, and has the potential to detect and resolve merged spots.
16
Comment
Find the spots using the pixel value collection