Batch Processing Images

Image analysis workflow

• Images grouped into batches by cropping system and date to maximize uniformity.
• When multiple images available, images selected for uniformity of exposure and color
• Occasional images possessed atypical color - in these cases, color balance was adjusted on a copy of the image, and both the original and copy were analyzed. (After review of false color images, the adjusted copy was retained only if classification was improved.) Note: We have fewer instances of this since we began using a DSLR camera in 2009 .
• Pixels sampled using a custom macro in ImageJ.
• Thresholds determined graphically for each batch of images (using R ). We used several custom functions in R to facilitate threshold determination.
• Images were batch processed using a shell script that called the C++ image analysis program and compiled the output.
• False color images reviewed to assure correct classification. Thresholds adjusted and batch processing repeated if needed.