1. Progressive Transmission of Two-Dimensional Gel Electrophoresis Image Based on Context Features and Bit-plane Method
Source:2004 IEEE International Conference
on Networking, Sensing and
Control,2004, pp
Authors:Tung-Shou Chen, Hsien-Chu Wu,
Hui-Fang Tsai, Mingli Hsieh and Shu-Fen
Chiou
Speaker:Shu-Fen Chiou(邱淑芬)
Date:2004/12/02
Mr. Chairman, Ladies and Gentlemen, I am honored to present my topic Progressive Transmission of Two-Dimensional gel Electrophoresis Image Based on context features and Bit-plan Method.
I am Shu Fen Chiou, I’m from National Taichung Institute of Technology Department of Information Management.
My supervisors are professor Tung-Shou Chen、Hsien-Chu Wu、Hui-Fang Tsai and Mingli Hsieh .
(1)As we know, two dimensional gel electrophoresis image is very important to a biologist.
(2)To be able to quickly transmit the image on the internet and to present it’s protein information is as important.
(3)Our purpose for this is research is to be able to transmit 2-D electrophoresis gel image quickly on the internet without losing the protein part of an image.

2. Outline 2D-gel Introduction Progressive image transmission methods
Bit-plane method
JPEG progressive compression coding model
Our Method
Experimental results
Conclusions
My paper include five parts.
The first is Introduction.
And the following are progressive image transmission methods, Our Method, Experimental results ,and Conclusions.

3. Introduction(1/2) Two-dimensional electrophoresis gel image
As shown ins a 2d---
The protein spots are the most important information.

4. Introduction(2/2)
Pixel value
(1)The distribution of an individual protein spot can be as shown an a x, y, z coordinates of a graph.
(2)The z-axis represents the pixel value.
(3)An interesting note:
The pixel value is characteristically distribute from inside-out, from small to big. y x

5. Progressive Image Transmission (PIT) methods
Bit-plane method (BPM).
JPEG progressive compression coding model.

6. Bit-plane Method First phase Second phase Third phase .
The bit-plane method is divided into 8 phases.
A gray pixel is normally 8 bits.
Bits are transmitted progressively from MSB to LSB.
First phase:
(a) If the first bit is 0, a pixel value 64 is assigned.
(b) If the first bit is 1, a pixel value 192 is assigned.
As you can see:
For the second phase:
(a) If the next bit is also 0, a pixel value 32 is assigned.
(b) Otherwise for bit 1, a pixel value 96 is assigned.
And so on…

7. JPEG progressive compression coding model8
DCT
The jpeg image is divided into 8x8 blocks
Goes discrete cosine transform
The coefficients in the blocks are progressively transmitted in zig-zag order. 8
Discrete cosine transform
Transmitted in zig-zag order
Divided into 8x8 blocks

8. Our method(1/8) Determine the Background Value Detect Protein Spots
Transmit the image progressively
Reconstruct the image

9. Our method(2/8) Background Value Average pixel value=
… /16
=187
221
190
200
182
185
170
178
199
202
231
188
175
180
168
155
221
190
200
182
185
170
178
199
202
231
188
175
180
168
155
Supposing a 4x4 image
We calculate the average pixel value, then we get 187
There are 7 pixels greater than 187
Background value is an average of these 7 pixels.
Background value=
… /7
=204
4x4 image

10. Our method(3/8) Detect Protein Spots A 5 6 7 4 0 3 2 1 7 1 2 5 3 4 2 4
Detect Protein Spots
We use the chain code idea to find the edge of an protein spot
Supposing we have a sample.
A is the first edge identified
Then we have 8 directions to find the next edge– the starting direction is clockwise from 0, 1, … to 7
And the next one, the next one, the next one
This is the final sequence we get
Chain code direction is clockwise from 0, 1, … to 7

11. Our method(4/8) Detect Protein Spot 8x8 image Background T1 = 30
average = 211
T1 = 30
T2 = 30
| | = 24 , 24 < 30
235
224
208
199
203
221
212
223
227
204
171
144
138
151
200
210
176
130 99 91
105
205
202
162
114 85 77
123
213
174
133
102
136
141
216
166
139
145
173
215
201
229
220
235
224
208
199
203
221
212
223
227
204
171
144
138
151
200
210
176
130 99 91
105
205
202
162
114 85 77
123
213
174
133
102
136
141
216
166
139
145
173
215
201
229
220
235
224
208
199
203
221
212
223
227
204
171
144
138
151
200
210
176
130 99 91
105
205
202
162
114 85 77
123
213
174
133
102
136
141
216
166
139
145
173
215
201
229
220
235
224
208
199
203
221
212
223
227
204
171
144
138
151
200
210
176
130 99 91
105
205
202
162
114 85 77
123
213
174
133
102
136
141
216
166
139
145
173
215
201
229
220
| | = 27 , 27 < 30
| | = 40 , 40 > 30
Suppose we have a 8x8 2d---
We have a protein spot
First we calculate its background average and we get 211
Threshold t1 is used to find the first edge
Threshold t2 will be used to locate other edges after the first edge
Now, we want to look for the first edge
Starting from the top first pixel, pixel value is 235
Taking the absolute value of background average minus the first pixel value
If result is greater than t1, the first edge is located, otherwise search somemore.
Once the first edge is located, we use the chain code idea together with t2 to locate all the other edges
If the absolute value of the first edge minus the pixel to its immediate right is less than t2 –this is the next edge
Otherwise clockwisely we calculate and search for the next edge
Protein spot
8x8 image

12. Our method(5/8) phase 1 Receiver Sender 8x8 image 8x8 image 56
235
224
208
199
203
221
212
223
227
204
171
144
138
151
200
210
176
130 99 91
105
205
202
162
114 85 77
123
213
174
133
102
136
141
216
166
139
145
173
215
201
229
220
235
224
208
199
203
221
212
223
227
204
171
144
138
151
200
210
176
130 99 91
105
205
202
162
114 85 77
123
213
174
133
102
136
141
216
166
139
145
173
215
201
229
220
211
180
149
118 87 56
(1,1)
(3,3) +
Background
(211)
In phase 1 ,we will transmit the top-left (1,1) , middle(3,3) and the bottom-right (6,5) coordinates together with the background average.
We will get this decompress result.
(6,5)
8x8 image
8x8 image

13. Our method(6/8) = - restore image difference original image 56
235
224
208
199
203
221
212
223
227
204
171
144
138
151
200
210
176
130 99 91
105
205
202
162
114 85 77
123
213
174
133
102
136
141
216
166
139
145
173
215
201
229
220
211
180
149
118 87 56
+24
+13 -3
-12 -8 +1
+12
+16 -7 -9 -5
-42
-60
-11 -1 -4
-27
-75
-73 -6
+27
+29
-10
-58
-88 +2
+15
+18
-39
-35 +5
-14
-25
-38
+10 +4 +9 = -
We taking the original image minus restore image and we get the difference
These difference values will be used to fix the image quality.
original image
restore image
difference

14. Our method(7/8) Receiver Sender . . 8x8 image phase 2 phase 2 phase 3
211
180
149
118 87 56 1
phase 2
phase 2
+24
+13 -3
-12 -8 +1
+12
+16 -7 -9 -5
-42
-60
-11 -1 -4
-27
-75
-73 -6
+27
+29
-10
-58
-88 +2
+15
+18
-39
-35 +5
-14
-25
-38
+10 +4 +9
211
180
149
118 87 56
phase 3
phase 3
In phase 2, we use the bit-plane method to transmit a bit map, with 0 for positive, 1 for negative, based on the difference table for the protein spot only.
Phase 3 through phase 10 is mapped from MSB through LSB
We have the original protein spot . .
8x8 image
204
171
144
138
151
200
176
130 99 91
105
162
114 85 77
123
174
133
102
136
141
208
166
139
145
173
210 1
phase 10
phase 10

15. Our method(8/8) Receiver Sender 8x8 image
211
204
171
144
138
151
200
176
130 99 91
105
162
114 85 77
123
174
133
102
136
141
208
166
139
145
173
210
+24
+13 -3
-12 -8 +1
+12
+16 -7 -9 -5
-42
-60
-11 -1 -4
-27
-75
-73 -6
+27
+29
-10
-58
-88 +2
+15
+18
-39
-35 +5
-14
-25
-38
+10 +4 +9
+24
+13 -3
-12 -8 +1
+12
+16 -1 -6 -9 +2 +5
+10
-11 +4
-10
+18 +9 1
phase 11
phase 11
211
204
171
144
138
151
200
176
130 99 91
105
162
114 85 77
123
174
133
102
136
141
208
166
139
145
173
210
phase 12
phase 12
For phase 11 we take the non protein spot areas and send a bit map of 0 for positive, 1 for negtive
Phase 12 through 19 is mapped from MSB through LSB
We have the complete 2d---
8x8 image . . . 1
235
224
208
199
203
221
212
223
227
204
171
144
138
151
200
210
176
130 99 91
105
205
202
162
114 85 77
123
213
174
133
102
136
141
216
166
139
145
173
215
201
229
220
phase 19
phase 19

16. Experiment results(1/8)
This is an original two-dimensional gel electrophoresis image.
512x512 original 2D image

17. Experiment results(2/8)
Phase 1:
Bit-plane Method JPEG model Our method

18. Experiment results(3/8)
Phase 2:
Bit-plane Method JPEG model Our method

19. Experiment results(4/8 )
Phase 3:
Bit-plane Method JPEG model Our method

20. Experiment results(5/8 )
Phase 4:
Bit-plane Method JPEG model Our method

21. Experiment results(6/8 )
Phase 5:
Bit-plane Method JPEG model Our method

22. Experiment results(7/8 )
Phase 6:
Bit-plane Method JPEG model Our method

23. Conclusions In comparison to the other two methods:
We can reveal a better image in lesser number of phases.
The total amount transmitted is smaller.