title: Enhanced CellClassifier: a multi-class classification tool for microscopy images.
abstract: BACKGROUND
  Light microscopy is of central importance in cell biology. The recent introduction of automated high content screening has expanded this technology towards automation of experiments and performing large scale perturbation assays. Nevertheless, evaluation of microscopy data continues to be a bottleneck in many projects. Currently, among open source software, CellProfiler and its extension Analyst are widely used in automated image processing. Even though revolutionizing image analysis in current biology, some routine and many advanced tasks are either not supported or require programming skills of the researcher. This represents a significant obstacle in many biology laboratories.
  
  
  RESULTS
  We have developed a tool, Enhanced CellClassifier, which circumvents this obstacle. Enhanced CellClassifier starts from images analyzed by CellProfiler, and allows multi-class classification using a Support Vector Machine algorithm. Training of objects can be done by clicking directly "on the microscopy image" in several intuitive training modes. Many routine tasks like out-of focus exclusion and well summary are also supported. Classification results can be integrated with other object measurements including inter-object relationships. This makes a detailed interpretation of the image possible, allowing the differentiation of many complex phenotypes. For the generation of the output, image, well and plate data are dynamically extracted and summarized. The output can be generated as graphs, Excel-files, images with projections of the final analysis and exported as variables.
  
  
  CONCLUSIONS
  Here we describe Enhanced CellClassifier which allows multiple class classification, elucidating complex phenotypes. Our tool is designed for the biologist who wants both, simple and flexible analysis of images without requiring programming skills. This should facilitate the implementation of automated high-content screening.
authors.affiliation: Institute of Microbiology, ETH Zurich, Zürich, Switzerland. misselwitz@micro.biol.ethz.ch
authors.forename: Benjamin
authors.initials: B
authors.lastname: Misselwitz
authors.forename: Gerhard
authors.initials: G
authors.lastname: Strittmatter
authors.forename: Balamurugan
authors.initials: B
authors.lastname: Periaswamy
authors.forename: Markus C
authors.initials: MC
authors.lastname: Schlumberger
authors.forename: Samuel
authors.initials: S
authors.lastname: Rout
authors.forename: Peter
authors.initials: P
authors.lastname: Horvath
authors.forename: Karol
authors.initials: K
authors.lastname: Kozak
authors.forename: Wolf-Dietrich
authors.initials: WD
authors.lastname: Hardt
mesh_terms: D016208:Databases, Factual; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008853:Microscopy / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods; D012984:Software