Wild Bug in CIA
Well... now I think I've seen it all. I found a bug in CIA today regarding the loading of a BMP file - basically, I had the red and blue bytes for each pixel reversed. How this showed up, however, is a tale to tell...
I have been trying to come up with an effective filter for the nuclear matter of the cells on the 7561/Her2 sample - you can see this on my CIA homepage. Basically, I can easily get the stained material, but the docs also want the number of cells, and their size to do a membrane comparison. So we've been trying to nail down what to look for. Well... today I hit on a big problem - the filter seemed to be acting exactly opposite to what I intended. I had computed HSL components of several RGB values, and the fat should have a high Hue, but was being nocked out by the high Hue filter. This was very troubling.
I checked the threshold calculations - they were right... then I checked the filters... they were right, and finally I got specific coordinates from GIMP and used them. I found the RGB values were wrong, and within five minutes, I realized that they were wrong in a very specific way - red and blue were transposed. Once I fixed it in the code the filter acted correctly. It was amazing... the data was bad in just such a way as to make the results look as if I had the binary filter in the wrong direction. How incredibly odd.
Now that I have the BMP reader working properly, I'm going back to look at some of the runs I've done to see if the Hue-based filters that didn't seem to work now work because the data is more in line. Preliminary results show that it's looking good and we could have made a big break-through today. What a trip!