An Online AI-Powered Interactive Histological Image Annotation Platform for Analyzing Intestinal Regenerating Crypts in Post-Irradiated Mice

Purpose/Objective(s)The goal of this project is to build an online AI-powered interactive annotation platform to accurately and efficiently annotate intestinal regenerating crypts in histological images of mice after abdominal irradiation.Materials/MethodsThe proposed platform is developed by the seamless integration of a front-end web client and a back-end server. Such client/server design allows the users to access the platform without software installation on local computers. Our front-end client is developed with SvelteJS + WebGL technology stack, allowing access from any common web browsers and enabling user interaction, such as image importing/visualization, interactive crypt annotating, and annotation saving/deleting. The back-end server is responsible for executing the tasks requested from the web client, for instance, image pre-processing, AI-based crypts automatic identification, and database management. The image preprocessing is designed to extract a single cross section image using morphological operations because multiple hematoxylin and eosin (H&E) stained jejunum cross sections from post-irradiated mice are scanned within one slide. The auto-crypt identification is powered by a trained and validated AI engine U-Net, classifying image grid tiles into two groups with and without regenerating crypts. The database is implemented with the self-contained SQLite to support recording and indexing the annotated grid tiles with regenerating crypts. The workflow for crypt analysis on this interactive platform has 5 steps: 1) manually import a whole H&E slide image; 2) auto-preprocess the slide by extracting single cross-section images; 3) auto-identify regenerating crypts with an AI engine; 4) interactively annotate (add, delete, modify) auto-identified crypt markers; 5) save and/or output the annotation to the database or the local drive.ResultsThe performance of the developed interactive crypt analysis platform was evaluated in aspects of accuracy and efficiency. The AI-powered crypt auto-identification accuracy was assessed by computing the mean absolute error (MAE) on crypt number per cross section between manual and auto annotation using a testing dataset containing 80 cross sections. It achieved an MAE of 3.5±4.8 crypts per cross section, and 81.25% of the cross sections have no more than 5 crypts difference. The efficiency was assessed under two conditions with the server on the cloud and a local computer. It took about 2-3 minutes to finish the entire workflow on the cloud, while 1-2 minutes on the local by saving ∼1 minute on image uploading.ConclusionThe developed web client/server platform enables online automatic identification and interactive annotation of mice crypts in minutes. It is a convenient tool that allows accurate and efficient crypt analysis and can be extended for other histologic image analyses. The goal of this project is to build an online AI-powered interactive annotation platform to accurately and efficiently annotate intestinal regenerating crypts in histological images of mice after abdominal irradiation. The proposed platform is developed by the seamless integration of a front-end web client and a back-end server. Such client/server design allows the users to access the platform without software installation on local computers. Our front-end client is developed with SvelteJS + WebGL technology stack, allowing access from any common web browsers and enabling user interaction, such as image importing/visualization, interactive crypt annotating, and annotation saving/deleting. The back-end server is responsible for executing the tasks requested from the web client, for instance, image pre-processing, AI-based crypts automatic identification, and database management. The image preprocessing is designed to extract a single cross section image using morphological operations because multiple hematoxylin and eosin (H&E) stained jejunum cross sections from post-irradiated mice are scanned within one slide. The auto-crypt identification is powered by a trained and validated AI engine U-Net, classifying image grid tiles into two groups with and without regenerating crypts. The database is implemented with the self-contained SQLite to support recording and indexing the annotated grid tiles with regenerating crypts. The workflow for crypt analysis on this interactive platform has 5 steps: 1) manually import a whole H&E slide image; 2) auto-preprocess the slide by extracting single cross-section images; 3) auto-identify regenerating crypts with an AI engine; 4) interactively annotate (add, delete, modify) auto-identified crypt markers; 5) save and/or output the annotation to the database or the local drive. The performance of the developed interactive crypt analysis platform was evaluated in aspects of accuracy and efficiency. The AI-powered crypt auto-identification accuracy was assessed by computing the mean absolute error (MAE) on crypt number per cross section between manual and auto annotation using a testing dataset containing 80 cross sections. It achieved an MAE of 3.5±4.8 crypts per cross section, and 81.25% of the cross sections have no more than 5 crypts difference. The efficiency was assessed under two conditions with the server on the cloud and a local computer. It took about 2-3 minutes to finish the entire workflow on the cloud, while 1-2 minutes on the local by saving ∼1 minute on image uploading. The developed web client/server platform enables online automatic identification and interactive annotation of mice crypts in minutes. It is a convenient tool that allows accurate and efficient crypt analysis and can be extended for other histologic image analyses.