This application is now outdated. Please see cukie/SMIA-CUKIE repository for the SMIA-CUKIE application. It can be thought of as v2. It's much more general to other use cases, can take a variable number of images as input, and has an easier-to-use graphical interface. While this version only analyzed RGB's, SMIA-CUKIE can take multiple image formats (most notably TIFFs) as monochramitic inputs.

java bulk imaging analysis of pathological immunofluourescent images

During the Summer of 2014 - collaboration with Dr. Franco-Barraza at Fox Chase Cancer Center to write a program that conducts digital quantitative and qualitative analysis in bulk. The developed algorithm batch-processes large sets of microscopic images, exports a corresponding database of resulting images representative of individual and combined color values images, and exports a full set of representative processed image results which match pre-set masks. The program also provides quantitative data such as specific and combinatorial customized color locations, intensities, averages, areas, and more, which can then be processed by a biostatistician. In this particular work, the output is being used to assess clinical relevance of particular protein marker levels in a large cohort of human pancreatic and kidney cancers. Current presentation and forthcoming peer reviewed paper:

Desmoplastic 3D-adhesion structures orchestrate... – publication in progress (current poster and presentation) J. Franco-Barraza1, T. Luong1, N. Shah1, R. Madhani1, G. Cukierman2, K. Alpaugh1, K. Devarajan1, J. Hoffman1, R. Uzzo1, E. Dulaimi1, E. Cukierman1;
1Fox Chase Cancer Center, Philadelphia, PA. 2University of North Carolina, Chapel Hill, NC. USA.

****NOTE: This is and was a working early version of the program. While all functionality is present, a more user friendly version, as well as some updates may exist. Please contact the Cukierman lab with all inquiries.