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Description

Java-based software and GUI to automatically manage/database large numbers of files (e.g., images) in a transparent file structure and perform batch processing with standard tools (ImageJ, R, Octave, Weka).

JEX Database Folder Structure

The organization of data in a JEX database goes like this... Repositories > Databases > Datasets > Entries > Objects.

• Databases are simply folders of Datasets with some extra xml files that represent the database structure.
• Datasets are simply folders of Entries.
• Entries are simply folders of Objects.
• Objects are simply folders of raw data files (e.g., tiff image files) and a single small *.arff formatted text file that JEX uses to keep track of how to organize the raw data files in that folder (e.g., many tiff files that represent time-points from a timelapse).

In this way, the files contained within an Object folder can be treated as an N-dimensional dataset. For example, a group of tiff files could be images that represent a mosaic of images taken in multiple colors, at multiple z-planes, at multiple times. The small .arff file in this folder keeps track of which images are for which location in the mosaic as well as which color, plane, and time. The number and name of dimensions of any Object is completely user defined in JEX.