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plugin:utilities:tapas:integrated_framework_for_automated_processing_and_analysis:start
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plugin:utilities:tapas:integrated_framework_for_automated_processing_and_analysis:start [2019/09/19 05:44] tboudier [Installation] |
plugin:utilities:tapas:integrated_framework_for_automated_processing_and_analysis:start [2019/09/19 05:55] tboudier [Features] |
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| Basically we will propose modules from the [[plugin:stacks:3d_ij_suite:start|3D ImageJ Suite]], ImageJ/Fiji, along with other modules. | Basically we will propose modules from the [[plugin:stacks:3d_ij_suite:start|3D ImageJ Suite]], ImageJ/Fiji, along with other modules. | ||
| - | We will propose, as a beta version, the following modules : | + | As for stable version 0.5 the following modules are available : |
| - | * Input/Output files (using BioFormats) | + | * Input/Output to files (using BioFormats) |
| * Input/Output to OMERO | * Input/Output to OMERO | ||
| * 3D filtering | * 3D filtering | ||
| - | * Auto-threshold and Iterative thresholding | + | * Auto-threshold, hysteresis and Iterative thresholding |
| * 3D labeling | * 3D labeling | ||
| - | * Objects measurements | + | * Objects measurements, signal quantification and numbering |
| + | * colocalisation and distances | ||
| * ImageJ macro | * ImageJ macro | ||
| Line 30: | Line 31: | ||
| - Install bioformats, either by downloading [[https://www.openmicroscopy.org/bio-formats/downloads/|bioformats_package.jar]] or by enabling the update site in Fiji. | - Install bioformats, either by downloading [[https://www.openmicroscopy.org/bio-formats/downloads/|bioformats_package.jar]] or by enabling the update site in Fiji. | ||
| - If you have an OMERO server, download [[https://www.openmicroscopy.org/omero/downloads/|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. | - If you have an OMERO server, download [[https://www.openmicroscopy.org/omero/downloads/|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. | ||
| - | - Download {{:plugin:stacks:3d_ij_suite:bundle-tapas0.51.zip|bundle-tapas0.5.zip}} and unzip it into the ImageJ or Fiji directory. | + | - Download {{:plugin:stacks:3d_ij_suite:bundle-tapas0.51.zip|bundle-tapas0.51.zip}} and unzip it into the ImageJ or Fiji directory. |
| TAPAS was tested successfully with OMERO.insight 5.5.5 and Bioformats 6.0.1. | TAPAS was tested successfully with OMERO.insight 5.5.5 and Bioformats 6.0.1. | ||
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| * How to quantify **layers distribution** [[plugin:utilities:layers_analysis:start|here]]. | * How to quantify **layers distribution** [[plugin:utilities:layers_analysis:start|here]]. | ||
| - | The list of available modules is described in {{:plugin:stacks:3d_ij_suite:tapasdescription0.5.pdf|TapasModules0.5.pdf}}. | + | The list of available modules is described in {{:plugin:stacks:3d_ij_suite:tapasdescription0.51.pdf|TapasModules0.51.pdf}}. |
| ===== 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 | ||
| Line 62: | Line 63: | ||
| ===== Change log ===== | ===== 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) | * 29/08/2019 V0.5 : stable version. New modules (see list) | ||
| * 06/05/2019 V0.41beta : fix bug in input/output on Windows | * 06/05/2019 V0.41beta : fix bug in input/output on Windows | ||
plugin/utilities/tapas/integrated_framework_for_automated_processing_and_analysis/start.txt · Last modified: 2019/09/19 05:55 by tboudier
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