Running BioImage.IO models in Fiji using DeepImageJ

Disclaimer: We've provided BioImage.IO versions of our main models to allow users to quickly test our models on their data without having to install new software. However, we highly recommend switching to our GelGenie application to be able to benefit from the main QOL features that are natively provided by QuPath and our own custom software.
To run GelGenie models released in BioImage.IO format, first install Fiji and then install the DeepImageJ plugin (instructions here).
Download a GelGenie model through the BioImage.IO interface within the plugin (search for GelGenie or else use our unique ids: self-disciplined-blowfish for the Universal model and trustworthy-llama for the fine-tuned model).
Load in your gel image. Make sure it is a single-channel image (if it's RGB, combine it using ImageJ's standard tools).
Select your image, then run the full_model_run.ijm macro in this folder to pre-process your image, run the model, post-process the results and generate a measurement for each band found in your image. Make sure to update the modelName variable to match the models you have downloaded first!
You can also run models directly from the DeepImageJ plugin or adjust our macro as you see fit.

Manually Accessing and Installing Models

You can directly download our models from BioImage.IO through the following links:
- Universal model: https://bioimage.io/#/?tags=gelgenie&type=model&id=self-disciplined-blowfish
- Finetuned model: https://bioimage.io/#/?tags=gelgenie&id=trustworthy-llama
We've also provided our models in BioImage.IO format for download on HuggingFace too:
- Universal Model: here
- Fine-Tuned Model (Sharp Band Model): here
To install in Fiji, download the models, select the install model manually option from the DeepImageJ extension toolbar, then point towards the downloaded zip files. After installation you'll be able to use the model as if it were downloaded from BioImage.IO.