Image Understanding Of Petri Dish Photos

I require an image loading, understanding, post-processing and saving program. I have a method for producing fairly uniform 5 megapixel images of a petri dish (aka petri plate). This is a circular plastic dish which contains a small amount of jello, on which bacteria form colonies. Because the photo may be taken at a slight angle, the circular plate looks ovoid (by a few pixels); and because it has some depth, these are not trivially concentric ovals. What I need to do is to find the constant elements in the image; that is, the edges of the plate and certain circular features on the plate's bottom, and remove them from the image. The image is cropped until the jello is visible and the circular features are 'erased' from the image. Then the image needs to be cleaned up in terms of contrast, and exported as one of several formats. I expect any programmer to use VXL or a similar library (like Aphelion) for the image loading, saving, and handling. However, anyone taking on this project should have image analysis experience. ## Deliverables What I am Providing: A sample image, many more available. Description of the Images: On a black background is a ?petri dish.? The wall of the plate is very bright. Radially inward, there is the reflective inner surface of the wall. There may be some irregular lighting on this surface. Then there is the dark edge of the ?media.' Finally, the ?field? is spotted with objects. On the sample image, they are dark on a red background. On other plates, the background may be beige, or they objects may be light on a darker red or beige background. Part way in, on this field, there is a ?stacking ring? that is barely visible on some pictures. A few pixels wide, it is two concentric rings, darker than the background. There can sometimes be seen a "falcon" watermark, which would be pleasent to remove, but removal of this is not part of the deliverables. Deliverables: A. With the weekly updates, I require the current code, to verify that progress is being made. Barring cancellation by buyer, this is transferred permanently. B. Complete and fully-functional working program in executable form (Windows) as well as source code (and makefiles, etc., for both Windows and RedHat). C. Complete copyrights. The coder may recycle his code for non-commercial projects or commercial projects that do not involve microbiology. He can use it for job applications. The programmer is expected to use libjpeg or a public domain library for the import and export of images, and VXL or an image understanding library for the processing of images. The program must: 1. Robustly find the elliptical (with deviations from circularity of up to 10% diameter) plate against the black background a. It cannot rely exclusively on hardcoded thresholds. b. It must still work if the plate touches the edge of the image. c. It must yield an intelligible error if there is no plate in the image. 2. Robustly find the junction between the edge of the plate and the media and crop the image at it. a. The plate ?wall? (and the mirror images which appear on it) are cropped out of the final image, but the real features ?inside,? on the media, are not. b. Errors in finding this junction must be limited to a couple pixels in diameter. c. I suggest finding a circle first, then looking for deviations from circularity and fitting a sine curve to them. 3. Find the ?stacking ring? and ?erase it? a. Coder's options include blurring or simply setting the pixel values to the same values as the lighter pixels immediately bordering it. The dark or light objects cannot be eliminated or split b. This needs to be user optional. 4. Output the cropped image a. ppm, tif, and jpeg b. Color options i. Full color ? crop the original image and erase the stacking ring in color ii. Greyscale ? crop the greyscale image and use an adaptive histogram to maximize contrast in the image iii. B/W ? use an adaptive threshold to make the objects either black on white or white on black 5. Processing Time: a. The new program should not take more than a minute per image on a 1 Ghz computer with 256 MB of RAM. b. This does not include loading the initial image into memory or saving to disk 6. User Inputs a. Option 1: single filename b. Option 2: directory -- output files get a name related to the original image names c. Option 3: list of files in a directory 7. Annotation (all algorithms, threshold values, constants and assumptions)in clear, precise English Verification, restricted to: A. 100 real plates being made and processed properly. If more than 3 plates which fall outside the standard (cropped within 2 pixels of the edge, the rings erased without splitting the objects on the field), the programmer may provide his progress for no fee, or fix the code. The images will be provided for debugging. 3 attempts (on fresh images) will be allowed. At 3 failures, the product becomes the property of the buyer at no cost. B. Reading the Annotation. ## Platform The platform for this program will be Windows and Linux. More precisely, Windows 2000, XP, 2003 Server; and RedHat. Verification will be performed under Windows 2000 or XP. Any windows project files should be compatible with VS .NET 2003