I'm reproducing here a section of the ECOCEAN Field Station Manual v2 related to pre-processing an image before spot extraction in order to start a discussion on standardized data processing to:
-minimize the likelihood of misidentification by using dual pattern recognition algorithms
-ensure processed images are easy to visually compare after the algorithms have been run by focusing only on the fiducial region and the remapping of matched spots to it
-promote the development of comparable images and digital patterns for those not using an online system, such as the ECOCEAN Library
This process adds a few steps many of you may not currently be incorporating into your own approach. We've found that images generated by this process are easy to visually compare and are compatible with the requirements of the I3S and modified Groth algorithms.
Let's discuss.
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Any encounter that is not assigned to a shark can have new left and/or right side spot data added to it in the ECOCEAN Library if properly oriented photos were submitted for it. Here are the steps required to extract a pattern from a photo for optimal pattern recognition using the I3S and modified Groth algorithms. Let’s use the following photo as a good example.
Figure 1. A new photograph submitted to the ECOCEAN Library.Pre-processing an image in Paint.NETIf you choose to use the free Paint.NET application to pre-process source images on Windows XP/Vista, use the following instructions. Alternative instructions for using
Adobe Fireworks (Windows/Mac) can be found in Appendix D of the ECOCEAN Field Station Manual version 2.0. If you're using a Linux system, the software package
GIMP offers similar functionality.
Paint .NET can be freely downloaded from:
http://fileforum.betanews.com/detail/PaintNET/1096481993/1 Paint.NET also requires installation of the Microsoft .NET Framework 2.0:
http://www.microsoft.com/downloads/details.aspx?familyid=0856eacb-4362-4b0d-8edd-aab15c5e04f5&displaylang=enFollow these steps to pre-process an image:
1. Open Paint.NET on your computer.
2. Open the picture in Paint.NET by selecting
Open from the
File menu.
Figure 2. A whale shark image loaded in Paint.NET.
3. Use the
Rectangle Select tool
to select the spot pattern area used for whale sharks.
Figure 3. Selecting the spot pattern area in Paint.NET.
4. From the
Image menu, select
Crop to Selection to reduce the image to only the needed patterning area.
Figure 4. A cropped spot pattern area.
5. We also recommend reducing the size of very large images to ensure the spot pattern area fits neatly onto the Paint.NET canvas at 100% magnification. To adjust image size, use the
Rectangle Select tool
to select the entire image and then select
Resize from the
Image menu. Adjust image size appropriately.
6. After obtaining a reduced image of only the spot pattern area, create a new layer to hold a horizontal adjustment line using the
Add New Layer button
of the
Layers pallet.
Figure 5. Adding a new layer to hold a reference line.
7. With the new layer selected in the Layers palette, add a horizontal reference line to the image using the
Line\Curve tool
. Hold the Shift key when drawing the reference line to ensure it is perfectly horizontal.
Figure 6. Adding a horizontal reference line.
8. Select the Background layer containing the cropped spot patterning area and then use the
Rectangle Select tool
to select the entire patterning area image. From the
Layers menu, select
Rotate/Zoom.
Figure 7. Adding a horizontal reference line.
9. Use the
Rotate and
Pan controls of the
Rotate/Zoom dialog box to rotate and move the spot patterning area until the vertebral column is flat against the horizontal line. Click
OK when you are done.
Note: The section of the vertebral column just above the fifth gill may curve downward slightly and not fit flush to the line. This is acceptable so long as the rest of the vertebral column above the pectoral fin is parallel to the line.
Figure 8. Obtaining a proper orientation for the spot patterning area.
10. Select the layer with the horizontal red line in the Layers pallet and click the
Delete Layer button
to remove it.
11. Use the
Rectangle Select tool
and the
Image,
Crop to Selection menu command to reduce you image to only the needed spot patterning area.
12. Choose
File,
Save As to save your completed processed image under a new name.
Figure 9. An image ready for spot pattern extraction.
You are now ready to extract the spots using I3S or Interconnect. Matched spots can easily be remapped to images such as these, focusing the eye on only the fiducial region and the results of scans for matches.
Figure 10. A match to H-019 made with the modified Groth algorithm. Potential spot pairs are marked with the same color in both images.
