Before you Start
- You'll need Java 8 (or better) installed on your computer. Most likely your computer already has this installed. But if not, got to http://java.com.
- Download the jar file to your computer.
- Double-click the jar to run the app.
You can also get the automated image analysis application here
Automated Image Analysis.
Just isn't there yet. That's why I developed the user interface below. Notes on what's been explored can be found here.
I'm working on a new method. Documentation is here
How to use it
Setup
Configure your settings. Some settings, such as the directory you want to save data into, are preserved between sessions.
Selection
Select the image you want to analyze along with the corresponding spot-definition (aka GAL) file. The application knows how to extract a single filter from a GAL that defines multiple filters. However, it assumes that all filters defined in a GAL are essentially identical.
Alignment
When you select an image and it's corresponding GAL, a new window will pop up overlaying the expected spots onto your image. Your job is to align the spots in the GAL with those on the image. Besides, rotation, scaling and translation of the spots, you can also increase the spot search area (aka diameter).
Alignment can be done directly on the image or using the sliders on the application
Aligning using Image Controls
Aligning using Slider Controls
Results
When you press the Analyze Image button, 2 data products are created:
- An image with the mean intensity values overlaid
- A tab-delimited text file with intensity statistics.
Each file is named after the image being analyzed. In addition, the filename has the UTC date that the sample was analyzed appended. For example, analyzing an image named filter_3.tif, will create files like filter_3-20090430221134.png and filter_3-20090430221134.txt.
 | How is the Intensity Calculated? The analysis results are based on:
A spot is analyzed as follows:
|
Image Result
Data Result
SpotNumber SourceWell Area Mean Median Std Min Max 1 M-1 9 49355.0 48604 3539.1 43383 54869 2 M-1 9 45450.4 45237 3079.1 40195 49597 9 A-1 9 5662.1 5543 276.5 5327 6037 10 A-1 9 5863.2 5859 276.8 5451 6288 11 M-1 9 46826.3 47433 3527.7 40002 51593 12 M-1 9 41673.3 41311 5130.4 30775 47634 13 C-1 9 5684.9 5703 105.0 5530 5827 14 C-1 9 5766.2 5758 134.0 5548 6039 33 A-1 9 5564.0 5639 214.3 5294 5845 34 A-1 9 5945.6 5931 188.0 5671 6170 35 A-1 9 6444.4 6452 246.2 6127 6893 36 C-1 9 5225.2 5162 207.0 4906 5492 37 C-1 9 5627.9 5539 330.1 5185 6376 38 C-1 9 5669.4 5615 231.1 5375 6160 57 M-1 9 48217.7 47461 6614.6 35229 55771 58 M-1 9 49192.3 49033 6575.7 35924 57107 59 A-1 9 6161.3 6159 190.3 5933 6543 60 A-1 9 5979.8 6066 345.0 5545 6597 61 A-1 9 7102.6 6759 1233.1 5967 9732 62 C-1 9 5487.8 5491 100.7 5355 5626 63 C-1 9 5570.3 5510 176.3 5255 5807 64 C-1 9 5459.4 5419 133.5 5235 5641 89 M-1 9 46842.1 48813 5160.4 37888 52613 90 M-1 9 47047.8 47124 4265.9 38956 52583 91 A-1 9 6272.9 6315 439.5 5284 6872 92 A-1 9 6121.4 6141 103.7 5941 6317 93 C-1 9 5494.0 5515 174.1 5303 5767 94 C-1 9 4985.1 4965 124.4 4803 5149 113 M-1 9 48944.3 49991 3707.7 42914 53405 114 I-1 9 25423.6 25613 1422.0 22955 27031 115 I-1 9 25197.3 25670 988.3 23421 26450 116 I-1 9 22132.4 22443 1272.5 19932 23443 117 K-1 9 51498.3 51759 2560.4 47191 55187 118 K-1 9 51888.1 52335 1953.1 49773 55666 119 K-1 9 52646.9 52985 2061.7 49485 55796 120 M-1 9 30787.3 30075 3475.8 23921 35206 121 M-1 9 34149.1 33959 2733.5 29768 37348 149 M-1 9 43475.1 43663 3603.0 38100 48773 150 M-1 9 44489.3 44609 3332.0 39065 49303 151 I-1 9 23479.1 23175 1384.3 20487 25171 152 I-1 9 24453.8 24841 1268.0 22381 25655 153 I-1 9 23526.8 23690 1187.2 21538 24913 154 I-1 9 21597.7 21709 1017.7 19604 22678 155 K-1 9 49745.0 50732 2936.6 44501 52759 156 K-1 9 47913.0 48388 2031.7 43423 50437 157 K-1 9 51569.7 51321 2375.2 48169 55215 158 K-1 9 52897.6 52851 2552.0 47967 56047 189 M-1 9 47880.7 49051 2907.6 44013 53047 190 I-1 9 24703.0 24444 708.3 23487 25453 191 I-1 9 23219.3 23389 1014.5 21703 24619 192 I-1 9 21817.2 22028 1010.8 19986 23403 193 K-1 9 54369.1 54732 3718.3 46532 58461 194 K-1 9 50194.6 50399 2553.9 45703 53492 195 K-1 9 45502.8 44757 2679.8 41538 48237 196 M-1 9 26627.3 27296 2518.6 22277 28987 197 M-1 9 31814.9 32016 1982.2 28295 34746 225 M-1 9 42895.4 43709 4152.5 34537 47623 226 M-1 9 39661.4 39303 3612.6 33975 44311 227 G-1 9 5144.4 5127 221.5 4734 5587 228 G-1 9 5070.7 5139 298.5 4457 5575 229 E-1 9 4945.2 4971 133.0 4764 5193 230 E-1 9 5207.7 5205 87.9 5085 5343 249 M-1 9 41336.3 42004 2850.3 35625 45492 250 M-1 9 37665.2 38325 2081.2 34699 40801 251 G-1 9 5331.7 5387 138.8 5093 5550 252 G-1 9 5594.6 5527 147.4 5398 5792 253 G-1 9 5012.8 5011 125.8 4869 5259 254 E-1 9 5017.9 5034 129.5 4703 5139 255 E-1 9 5810.6 5767 466.6 5395 6926 256 E-1 9 5415.9 5379 171.3 5195 5705 281 G-1 9 4841.2 4835 145.3 4635 5095 282 G-1 9 5204.3 5143 146.4 5015 5403 283 G-1 9 5278.7 5249 271.8 4974 5822 284 E-1 9 5187.6 5143 135.8 5083 5519 285 E-1 9 5257.4 5282 66.5 5113 5323 286 E-1 9 4652.3 4648 151.5 4414 4918 305 G-1 9 4980.6 4964 168.7 4751 5307 306 G-1 9 4723.1 4763 82.8 4591 4804 307 M-1 9 27011.7 27094 1546.5 23564 28924 308 M-1 9 27658.3 28069 1809.2 24951 29929 309 E-1 9 4644.2 4662 80.3 4523 4731 310 E-1 9 4403.9 4429 134.1 4148 4559 329 M-1 9 33267.1 32311 3910.5 25015 36996 330 M-1 9 31966.2 33229 3090.1 26878 35366
filter_3-20090430221134.png (image/png)
ESPImageMeasurement-sliderControl.png (image/png)
ESPImageMeasurement-setup.png (image/png)
ESPImageMeasurement-selection.png (image/png)
ESPImageMeasurement-imageControl.png (image/png)
