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.
Image Analysis Workflow