TAPAS your new companion for batch processing

fiji
imagej
batch-processing

#1

Dear image processing and analysis enthusiasts,

I am glad to announce the release of TAPAS. TAPAS (Towards an Automated Processing and Analysis System) is an easy to use batch processing system for your every day need.

It is based on a list of simple modules that you chain together to create your processing pipeline, no programming or complex linking required, just good old text file. It will include most of the functionalities of the 3D ImageJ Suite.

Curious ? Have a look at the TAPAS website, tutorials included.

Feedback and comments welcome !

Thomas


#2

I didn’t read the pages too thoroughly, so it is possible I may have missed the answer to my question.

It seems to me that this framework provides convenient use of certain modules and I/O for OMERO. However, can it work with multiple images at once or is it limited to one at a time (like ImageJ’s built-in batch processor)? For example, would I be able to subtract one image from another using this framework?


#3

Hi @Andrew_Shum,

This framework is a simplified batch processing system with focus on OMERO I/O. By default, it will process one image at a time, but by using temporary files you can perform operation between images. Actually the math module is already written but hidden :wink: , you can use it by adding this line to the file tapas.txt math:mcib3d.tapas.plugins.processing.ArithmeticProcess . I use it to perform operations between channels, here an example :

// input first channel and save it
process:input
channel:0
process:save
dir:?ij?
file:C0.tif
// input other channel and then subtract C0
process:input
channel:1
// Arithmetic operation
process:math
dir:?ij?
file:C0.tif
operation:add
coef0:1.0
coef1:-1.0

I hope to release other examples and tutorials over the following weeks. Stay tuned !

Best,

Thomas