TAPAS (Towards an Automated Processing and Analysis System) is a framework for processing and analysis workflow for multi-dimensional images. A workflow is a series of modules linked together to process an image, each module should perform one simple task.
The first idea is to design a framework where users can share the pipeline as simple text file. The second idea is to create a simple programming template so developers can create their own module.
Finally, the pipeline should be separated from the set of images to process, so a same pipeline can be used for different images. The results of the processing and the analysis should be stored along with the processed images.
Here we propose modules to process and analyze images stored in an OMERO database, but the system should work fine with files stored locally or on a server.
Basically we will propose modules from the 3D ImageJ Suite, ImageJ/Fiji, along with other modules.
We will propose, as a beta version, the following modules :
TAPAS was tested successfully with OMERO 5.4.9 and Bioformats 5.7.3.
A list of tutorials :
The list of available modules are described here.
2018 Whitehead, L., Wimmer, V., Lafouresse, F., Ratnayake, D., Currie, P., Groom, J., Rogers, K. and Boudier, T. Towards an Automated Processing and Analysis System for multi-dimensional light-sheet microscopy big data using ImageJ and OMERO. International Microscopy Congress IMC 19. (pdf)
Beta version is not GPL and source code is not available. Stable version will be under GPL distribution (see license), and source code will be available on GitHub.