Seitenhistorie

Requirements:

• Data uploaded to OMERO (OMERO upload)
• Fiji plugin for OMERO installed (1. Export OMERO images to FIJI)

1. Create tag in OMERO

Create a tag in the group where the images are located. Suggestions to name the tag:

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Tags can be renamed after creation. In the case more than one "training tag" exists, we recommend placing them inside a "tag set" in OMERO

2. Assign tag to selected images

To make a good training set, randomly select images from all your datasets and assign the training tag to them. 

The training set needs to cover as much variability that exists in your data, in order to give a chance to your model to generalize classification to future data.

3. Open images from Fiji

• Following the instructions in 1. Export OMERO images to FIJI, connect to OMERO.
• Browse the data by tags, and find your images under the "training tag":

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• Right click on images → "View in ImageJ"
• Make your ROIs and add them to the ROIManager (ctrl+T)

4. Export ROIs to OMERO

• When finished with all ROIs of an image, export the ROIs to OMERO (2. Export FIJI ROIs to OMERO)

5. Generate the training dataset

• Images and ROIs living inside OMERO, we need to export them to a local folder (training a model can be resource intensive, it's more efficient to avoid loading the same image over and over from the server)
• Install the OMERO macro extension ()
• You can create your own macro to loop over every images having the tag (find the tag ID), read their ROIs and export images and masks locally.

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