= Create OMERO.tables from a csv file =
==**Description:**==
**OMERO.tables** unifies the storage of columnar data from various sources, such as automated analysis results or script-based processing, and makes them dynamically available within OMERO.
==**Ressources:**==
**Dataset**: Copy the folder called {nav NEDD} 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
**CSV file**: Copy the file //four-NEDD-images.csv// from:
WIN: \\svfas6.epfl.ch\biop\public\0-BIOP_Data\0-Install\OMERO\demo extra files
MAC: smb://svfas6.epfl.ch/biop/public/0-BIOP_Data/0-Install/OMERO/demo extra files
==Step-by-Step:==
# Upload the folder called {nav NEDD} to OMERO **as a Dataset** and in OMERO, name this dataset NEDD.
# In OMERO.web, attach the //four-NEDD-images.csv// file to your NEDD Dataset using the {nav +} button under the {nav Attachments} harmonica from the right panel. {F20393539, width=300, style=inline}
# Select the NEDD dataset and click on the {icon cogs} button** from the top menu bar of omero web **.
# Go to {nav import_scripts > Populate Metadata...}. Run the script
# Select the NEDD dataset from the left-hand pane and observe in the right hand pane under “Attachments” that there is a new file called //bulk_annotations// attached to your NEDD dataset. This is your newly created OMERO.table, that can be opened from the web by hitting the {icon eye} button. It contains in each line a dynamic link to the corresponding image in OMERO.web {F20393719, width=500}
Back to OMERO.web's main page, clic on one of the images from the {nav NEDD} dataset without opening it 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. {F20393728, width=300}
= 2. Create OMERO.tables from FIJI's scripting editor =
See [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/analysis/fiji/ | alyze OMERO data in batch using the Scripting editor in Fiji]]
= 3. Analyze metadata using OMERO.parade =
==Description:==
**OMERO.parade** is a metadata-mining plugin for OMERO.web. It enables access to the metadata of images in OMERO for plotting, display and filtering of images. Supported metadata includes number of ROIs, Key-Value pairs, and data stored in OMERO.tables.
**OMERO.tables** unifies the storage of columnar data from various sources, such as automated analysis results or script-based processing, and makes them dynamically available within OMERO.
==Resources:==
Sample images from the Image Data Resource (IDR) idr0021. See idr0021-data-prep.md for download and import instructions.
Sample plate data from Plate with 422 on IDR from idr0002. Use the script idr_copy_plate.py to copy Plate ID 422. Run the script with $ python idr_copy_plate.py username password 422 --server your.server.org
==Step-by-Step:==