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.
Author
Features
Basically we will propose modules from the 3D ImageJ Suite, ImageJ/Fiji, along with other modules.
As for stable version 0.5 the following modules are available :
Input/Output to files (using BioFormats)
Input/Output to OMERO
3D filtering
Auto-threshold, hysteresis and Iterative thresholding
3D labeling
Objects measurements, signal quantification and numbering
Colocalisation and distances
Calling ImageJ macros
Installation
-
Install
3D ImageJ Suite. It is also available as a update site in Fiji.
ImageScience should be installed too, either from
here or via the update site in Fiji.
-
If you have an OMERO server, download
OMERO-insight, unzip OMERO.insight-ij-xxx.zip into the plugins directory of ImageJ or Fiji. The version number should match the version number of your server. Please do not install OMERO-insight from the Fiji update site.
-
TAPAS was tested successfully with OMERO.insight 5.5.5 and Bioformats 6.0.1.
Usage / Tutorials
If you want to process data stored on an Omero server, connect first to your server using TAPAS Connect inside the TAPAS menu.
Create your pipeline in a text editor, check available tapas modules and how to use it in the documentation provided.
Run TAPAS OMERO if you want to process data from Omero or TAPAS FILE for data on files.
A list of tutorials :
Basic
Input/Ouptput functionalities
here.
Create your first
processing pipeline here.
Segmentation modules
here.
Measurement modules
here.
Signal quantification and
numbering modules
here.
-
How to use the
analyzeParticles module for segmentation and measurement
here.
How to quantify
layers distribution here.
The list of available modules is described in TapasModules0.51.pdf.
Citation
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)
License
Change log
19/09/2019 V0.51 : minor change, new module load attachment from Omero
29/08/2019 V0.5 : stable version. New modules (see list)
06/05/2019 V0.41beta : fix bug in input/output on Windows
05/03/2019 V0.4beta : channels and frames now start at 1, new binning option in Omero Load, module 3dfilters is renamed filters and has parameter radxy (instead of radx and rady), new tutorials on measurements and quantification
01/02/2019 V0.3beta : first beta release