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plugin:utilities:tapas_:integrated_framework_for_automated_processing_and_analysis:start [2019/01/10 06:34]
tboudier [Usage]
plugin:utilities:tapas_:integrated_framework_for_automated_processing_and_analysis:start [2019/01/21 05:59] (current)
tboudier [Usage]
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 ===== TAPAS : An integrated tool for processing and analysis using ImageJ and OMERO (beta) ===== ===== TAPAS : An integrated tool for processing and analysis using ImageJ and OMERO (beta) =====
- 
 TAPAS (Towards an Automated Processing and Analysis System) is a framework for processing and 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.  TAPAS (Towards an Automated Processing and Analysis System) is a framework for processing and 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. 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 same pipeline can be used for different images. The results of the processing and the analysis should be stored along with the processed images.+Finally, the pipeline should be separated from the set of images to process, so 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 analyse images stored in an OMERO database, but the system should work with files stored locally or on a server. Here we propose modules to process and analyse images stored in an OMERO database, but the system should work with files stored locally or on a server.
 +
 ===== Author ===== ===== Author =====
 Thomas Boudier Thomas Boudier
  
 ===== Features ===== ===== Features =====
- 
 Basically we will propose modules from the [[plugin:stacks:3d_ij_suite:start|3D ImageJ Suite]] along with other modules. Basically we will propose modules from the [[plugin:stacks:3d_ij_suite:start|3D ImageJ Suite]] along with other modules.
  
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   * ImageJ macro   * ImageJ macro
  
-The list of available modules are described {{:plugin:stacks:3d_ij_suite:tapasdescription.pdf|here}}. 
-===== Usage ===== 
-     - Connect to your Omero server using** TAPAS Connect** inside the TAPAS menu. 
-     -  Create your pipeline in a text editor, check available tapas 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. 
  
 ===== Installation ===== ===== Installation =====
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      -  Download {{:plugin:stacks:3d_ij_suite:bundle-tapas.zip|bundle-tapas.zip}} and unzip it into the ImageJ or Fiji directory.      -  Download {{:plugin:stacks:3d_ij_suite:bundle-tapas.zip|bundle-tapas.zip}} and unzip it into the ImageJ or Fiji directory.
  
 +===== Usage =====
 +     - Connect to your Omero server using** TAPAS Connect** inside the TAPAS menu.
 +     -  Create your pipeline in a text editor, check available tapas 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 **tutorial** for basic Input/Ouptput functionalities is available [[plugin:utilities:tapas_tutorial_:input_output_i:start|here]].
 +  * A **tutorial** to create your first processing pipeline is available [[plugin:utilities:tapas_tutorial_:create_your_processing_pipeline:start|here]].
  
 +The list of available modules are described {{:plugin:stacks:3d_ij_suite:tapasdescription.pdf|here}}. 
 ===== Citation ===== ===== Citation =====
 2018 Whitehead, L., Wimmer, V., Lafouresse, F., Ratnayake, D., Currie, P., Groom, J., Rogers, K. and 2018 Whitehead, L., Wimmer, V., Lafouresse, F., Ratnayake, D., Currie, P., Groom, J., Rogers, K. and
plugin/utilities/tapas_/integrated_framework_for_automated_processing_and_analysis/start.1547098491.txt.gz · Last modified: 2019/01/10 06:34 by tboudier
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