BioImage Model Zoo Connection

🦒 BioImage Model Zoo Connection

Introduction

The BioImage Model Zoo is a community-driven AI model repository. The aim is to facilitate the adoption of AI methods among the bioimaging community by providing easy access to pretrained AI models. By establishing a common Model Resource Description File Specification, the model zoo serves as a distribution point for deep learning models trained to perform bioimage analysis tasks.

In regards to deepImageJ, the BioImage Model Zoo serves as an AI model repository whose models can be easily downloaded and installed into the deepImageJ plugin to test them with your own images. The format of the BioImage Model Zoo models ensures compatibility between the two software applications.

Prerequisites

Before connecting to the BioImage Model Zoo, ensure that you have the following:

• A working installation of Fiji.
• The deepImageJ plugin installed and configured.
• Internet access to download models from the BioImage Model Zoo.

Downloading and Using Models from the BioImage Model Zoo

Connecting to the BioImage Model Zoo

1. Locate BioImage Model Zoo model: Go to bioimage.io. A window will open, displaying the available models in the BioImage Model Zoo. You can browse through the different categories or use the search function to find a specific model suitable for your analysis.

2. Download a Model: Once you have located a model, open its model card, click to Download and in Download by software select the one for deepImageJ. It will be downloaded to your Downloads/ folder.

   If you already know which model you want to download, you can directly download it from the deepImageJ plugin following the next step.

3. Install Model to deepImageJ: Open Fiji and then navigate to Plugins > deepImageJ > deepImageJ Install Model to open the installer of models of deepImageJ. Once you are here, you have two options:

   a. If you have downloaded the model following step 2, you can go to the tab Private Model, select From ZIP file and put the location of your model including the model file. For example, you would write User/Downloads/Your_BMZ_model.zip. Read and agree to the text at the bottom and select Install.

   b. If you want, you can directly select a model from the BioImage Model Zoo tab through Select a compatible model. Select your model, read and agree to the text at the bottom and select Install.

Using Downloaded Models

1. Load the Model: To run a model, in Fiji, navigate to Plugins > deepImageJ > deepImageJ Run. Once there, if you have installed a model, go to the Models section and locate the model you just downloaded from the BioImage Model Zoo. Note that if you open deepImageJ Run after installing a model, it can take a while as it is installing it.

2. Configure Model Parameters: Depending on the model, you may need to configure specific parameters such as Format, Preprocessing, or Postprocessing steps.

3. Apply the Model: Open the image you want to analyze in ImageJ. Select the configured model from the deepImageJ plugin and apply it to your image. The results will be displayed in a new window or overlaid on the original image.

Troubleshooting

If you encounter issues while connecting to or using models from the BioImage Model Zoo, consider the following steps:

• Check Internet Connection: Ensure that your computer has a stable internet connection to download models from the BioImage Model Zoo.

• Verify Compatibility: Make sure that the model you are trying to download is compatible with your version of ImageJ and deepImageJ.

• Consult Documentation: Refer to the official deepImageJ and BioImage Model Zoo documentation for additional troubleshooting tips and support.

If you have problems installing a model from the BioImage Model Zoo that you have just downloaded, you can try to install it manually. To do so, open your Fiji folder and locate the models folder. Drag and drop your zip file containing your model to the models folder and unzip it inside this folder. Now continue as if you had installed it with the normal process.

Conclusion

Integrating deepImageJ with the BioImage Model Zoo significantly enhances your bioimage analysis capabilities by providing easy access to a wide range of pre-trained deep learning models. Follow the steps outlined above to connect to the Model Zoo, download models, and apply them to your image data for efficient and accurate analysis.

For more information, visit the BioImage Model Zoo and the deepImageJ websites.