This guide demonstrates how to access and analyze your OMERO images using the official OMERO plugin for Fiji, as well as how to perform batch analysis on OMERO datasets using Fiji's scripting facility.
= Analyze OMERO data using the OMERO plugin for Fiji =
===** OMERO plugin installation in Fiji**===
We assume that you have already Fiji/ImageJ installed locally.
Installing the OMERO plugin in Fiji also adds the dependencies required to connect to OMERO using the Script Editor of Fiji.
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**Step-by-step**
# Find the Plugins folder of your Fiji application and check if it contains any old omero_ij-5.x.x-all.jar file(s) or OMERO.imagej-5.x.x folder(s). Remove any such jar files or folders from the Plugins folder.
# Download from https://www.openmicroscopy.org/omero/downloads the latest 5.x.x version of ImageJ/Fiji plugin for OMERO
# Note where you downloaded the omero_ij-5.x.x-all.jar file. Copy that file into the plugins folder of Fiji.
# Now, restart Fiji. The plugin is ready to use: In Fiji, you can find it in {nav Plugins > OMERO > Connect to OMERO}
===** Segment and analyze OMERO data manually with the plugin **===
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= Analyze OMERO data in batch using the Scripting editor in Fiji =
===** Setup **===
Install Fiji and the OMERO plugin for Fiji (see //OMERO plugin installation in Fiji// above).
===** Ressources **===
**Data**: Copy and import to OMERO the folder called {nav EdU RFP} from:
WIN: \\svfas6.epfl.ch\biop\public\0-BIOP_Data\0-Install\OMERO\demo dataset analysis v2
MAC: smb://svfas6.epfl.ch/biop/public/0-BIOP_Data/0-Install/OMERO/demo dataset analysis v2
**Scripts**:
Groovy script for running a macro in batch (on a whole OMERO dataset) using Fiji:
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Example analysis macro file (segmentation + positive cell counts in 2 channels):
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===** Step-by-Step **===
# Download the {nav EdU RFP} dataset and the scripts. Upload the {nav EdU RFP} dataset to OMERO.
# Drag and drop the `Dataset_Macro-ROIs_Summary.groovy` file in FIJI (or go to {nav Files > Open...}) to open the script in FIJI's scripting editor.
# Hit {nav Run}
# Enter your gaspar credentials and check that the hostname is correct (omero-server.epfl.ch) {F20244042, layout=inline, width=300}
# Go to OMERO.web to check the ID of your {nav EdU RFP} dataset in OMERO. Enter this ID in the {nav Dataset ID} field.
# For the Macropath field, browse through your downloaded files and select the `Workflow_segmentation_macro_nosplit_countposcells.ijm` macro file.
# Let the script run and go back to the {nav EdU RFP} dataset on OMERO.web when it is finished. Open an Image from this Dataset in OMERO.iviewer. Click the ROIs tab to see the added ROIs. {F20244197, layout=inline, size = full} Back to OMERO.web's main page, select the {nav EdU RFP} dataset from the left-hand tree. Look at the {nav Attachments} harmonica from the right-hand pane. The Summary table from FIJI has been attached to the dataset as a .csv file that can be downloaded, but also as an OMERO.table (Summary_from_Fiji) that can be viewed from the web by hitting the {icon eye} button. {F20244194, layout=inline, width=300}
Open the OMERO.table (Summary_from_Fiji) by hitting the {icon eye} button. It contains in each line a dynamic link to the corresponding image in OMERO.web.
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Back to OMERO.web's main page, clic on one of the images from the {nav EdU RFP} without opening in with the iviewer. Look at the {nav Tables} harmonica from the right-hand pane. Observe that all the statistics from the OMERO.table that apply to the selected image are gathered here.
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