ATI_Box: A Simple tool for convolutional neural network-based image semantic segmentation

Abstract

Quantitative analysis of microscopic images has become a standard in basic biological and biomedical research. Deep machine learning provided a powerful tool facilitating this process. However, practical adoption of deep machine learning to image analysis may be difficult for a researcher who lacks basic coding skills. This is caused by a limited number of non-coding solutions, specifically in the domain of convolutional neural networks (CNNs). This scarcity may be explained by the following paradox. Training of CNNs is a relatively complex process. Researchers who are familiar with this process are also skilled enough to code the full pipeline of CNN implementation from annotation, through model training and evaluation to its usage in laboratory practice. Any kind of an alternative solution, acceptable by a broader group of researchers who are unfamiliar with CNN concepts, must inevitably result in simplification of the entire process, specifically the training step. Such simplification in turn may lead to limitation to solve specific problems by such a tool. Author believes however, that some compromise may be found between complexity and simplicity that would be sufficient to solve some basic problems in the field of basic biological and biomedical research. To address this challenge, author proposes ATI_Box (Annotation, Training, Inference in One Box), a unified, user-oriented platform for end-to-end image semantic segmentation. The system integrates data annotation, storage, model training, evaluation, and quantitative analysis into a single workflow, significantly simplifying the model development process. Image and annotation data are managed through an S3-compatible object storage system (MinIO), enabling scalable and transparent data handling. Annotation process is implemented through Label Studio. Model training is based on convolutional neural network U-Net architecture with ResNet as an encoder. Model evaluation is performed on ground-truth dataset held-out during training and provides pixel-level and object-level evaluation metrics. Batch analysis mode enables automated quantification of model predictions such as object counts and coverage areas. The usability of the platform was presented on examples from laboratory practice. The platform is intentionally devoid of model-tuning capabilities as it is addressed to users unfamiliar with profound machine learning concepts. At the same time, accessibility of such basic features of model training as definition of epochs number or saving and implementing of trained model versions enables one to perform some basic analytical experiments. As such, the platform may serve not only as an analytical tool but also as an educational solution to explain practical basics of semantic segmentation process.