Abstract
Modern microscopy is based on reproducible quantitative analysis, image data should be batch-processed by a standardized system that can be shared and easily reused by others. Furthermore, such system should require none or minimal programming from the users. We developed TAPAS (Towards an Automated Processing and Analysis System). The goal is to design an easy system for describing and exchanging processing workflows. The protocols are simple text files comprising a linear list of commands used to process and analyse the images. An extensive set of 60 modules is already available, mostly based on the tools proposed in the 3D ImageJ Suite. We propose a wizard, called TAPAS menu, to help the user design the protocol by listing the available modules and the parameters associated. Most modules will have default parameters values for most common tasks. Once the user has designed the protocol, he/she can apply the protocol to a set of images, that can be either stored locally or on a OMERO database. An extensive documentation including the list of modules, various tutorials and link to the source code is available at https://imagej.net/TAPAS.
Highlights
Introduction to3D Analysis with 3D ImageJ Suite
First category of automation methods is script-based automation, such as ImageJ or ICY scripts, both based on Java or JavaScript language
We developed TAPAS (Towards an Automated Processing and Analysis System) as a system for describing and exchanging processing workflows
Summary
Any further responses from the reviewers can be found at the end of the article Introduction Modern microscopy, through new systems like light-sheet or high-throughput microscopes, is generating a vast amount of complex data that needs to be analysed. First category of automation methods is script-based automation, such as ImageJ or ICY scripts, both based on Java or JavaScript language These scripts will include reference to location of data itself and are not shared between users. Second category is graph-based automation, such as ICY protocols or CellProfiler They are quite easy to apprehend for inexperienced users, it may not be straightforward, due to the intrinsic graph structure of the workflows, to build complex processing pipelines. With the spread of database systems such as OMERO5, more and more imaging facilities and labs are storing their data in a more organized fashion
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