Example Usage and Tutorials

📚 Example Usage and Tutorials

Introduction

The DeepImageJ case studies repository contains various examples demonstrating how to use DeepImageJ for different bioimage analysis tasks. These case studies illustrate the application of deep learning models for image-to-image translation, nuclei segmentation, and integration with the BioImage Model Zoo. Each example includes scripts, macros, and detailed instructions to replicate the workflows.

Case Study 1: Pipeline for Integrated Image-to-Image Translation and Nuclei Segmentation

Details

• Description: This case study demonstrates the use of deepImageJ for performing image-to-image translation from actin to DAPI images, followed by nuclei segmentation using the StarDist model. The pipeline is then integrated into a macro for batch processing.
• Files:
  • prepare_dataset.py: Script for preparing the dataset for image-to-image translation and segmentation.
  • StarDist_Postprocess_macro_CS1.ijm: ImageJ Macro for StarDist post-processing in Case Study 1.
• Notebooks: Pix2Pix and StarDist 2D from ZeroCostDL4Mic.
• Dataset: Pix2Pix, Lifeact-RFP actin stain images and StarDist, sir-DNA dapi stain images
• Models: Pix2Pix for Image Translation from Lifeact-RFP to sir-DNA and StarDist Model for Nuclei Segmentation in Synthetic Lifeact-RFP

Step by Step

Case Study 2: Comprehensive 3D Nuclei Segmentation with deepImageJ

Details

• Description: In this case study, deepImageJ is utilized for detailed 3D nuclei segmentation, showcasing its capability in handling complex volumetric data. The pipeline involves the generation of ground truth data, followed by the use of StarDist for nuclei segmentation. The pipeline is then integrated into a macro for batch processing.
• Files:
  • Generated_GT.py: Script for generating ground truth data for 3D nuclei segmentation.
  • Mount_stardist_dataset.py: Script for setting up the StarDist dataset for 3D segmentation.
  • StarDist_postprocess_macro_cs2.ijm: ImageJ Macro for StarDist post-processing in Case Study 2.
• Notebooks: StarDist 2D
• Dataset: Developing Tribolium Castaneum Embryo from Cell Tracking Challenge
• Model: StarDist Model for Developing Tribolium Castaneum Embryo

Step by Step

Case Study 3: Segmentation of Arabidopsis Apical Stem Cells and Integration with the BioImage Model Zoo in deepImageJ

Details

• Description: This case study involves the segmentation of Arabidopsis apical stem cells and demonstrates the integration with the BioImage Model Zoo using deepImageJ.
• Dataset: Research data supporting Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche
• Models: 3D Unet Arabidopsis Apical Stem Cells with emotional-cricket ID for the BioImage Model Zoo

Step by Step