DeepClas4Bio: Connecting bioimaging tools with deep learning frameworks for image classification

DeepImageJ: A user-friendly environment to run deep learning models in ImageJ

DeepImageJ is a user-friendly solution that enables the generic use of pre-trained deep learning models for biomedical image analysis in ImageJ. The deepImageJ environment gives access to the largest bioimage repository of pre-trained deep learning models (BioImage Model Zoo). Hence, nonexperts can easily perform common image processing tasks in life-science research with deep learning-based tools including pixel and object classification, instance segmentation, denoising or virtual staining. DeepImageJ is compatible with existing state of the art solutions and it is equipped with utility tools for developers to include new models. Very recently, several training frameworks have adopted the deepImageJ format to deploy their work in one of the most used softwares in the field (ImageJ). Beyond its direct use, we expect deepImageJ to contribute to the broader dissemination and reuse of deep learning models in life sciences applications and bioimage informatics.

Quantitative Approaches to Study Retinal Neurogenesis

The study of the development of the vertebrate retina can be addressed from several perspectives: from a purely qualitative to a more quantitative approach that takes into account its spatio-temporal features, its three-dimensional structure and also the regulation and properties at the systems level. Here, we review the ongoing transition toward a full four-dimensional characterization of the developing vertebrate retina, focusing on the challenges at the experimental, image acquisition, image processing and quantification. Using the developing zebrafish retina, we illustrate how quantitative data extracted from these type of highly dense, three-dimensional tissues depend strongly on the image quality, image processing and algorithms used to segment and quantify. Therefore, we propose that the scientific community that focuses on developmental systems could strongly benefit from a more detailed disclosure of the tools and pipelines used to process and analyze images from biological samples.

Bioimage Analysis and Cell Motility

Bioimage analysis (BIA) has historically helped study how and why cells move; biological experiments evolved in intimate feedback with the most classical image processing techniques because they contribute objectivity and reproducibility to an eminently qualitative science. Cell segmentation, tracking, and morphology descriptors are all discussed here. Using ameboid motility as a case study, these methods help us illustrate how proper quantification can augment biological data, for example, by choosing mathematical representations that amplify initially subtle differences, by statistically uncovering general laws or by integrating physical insight. More recently, the non-invasive nature of quantitative imaging is fertilizing two blooming fields: mechanobiology, where many biophysical measurements remain inaccessible, and microenvironments, where the quest for physiological relevance has exploded data size. From relief to remedy, this trend indicates that BIA is to become a main vector of biological discovery as human visual analysis struggles against ever more complex data.

Biomedical image classification made easier thanks to transfer and semi-supervised learning

BACKGROUND AND OBJECTIVES

Deep learning techniques are the state-of-the-art approach to solve image classification problems in biomedicine; however, they require the acquisition and annotation of a considerable volume of images. In addition, using deep learning libraries and tuning the hyperparameters of the networks trained with them might be challenging for several users. These drawbacks prevent the adoption of these techniques outside the machine-learning community. In this work, we present an Automated Machine Learning (AutoML) method to deal with these problems.

METHODS

Our AutoML method combines transfer learning with a new semi-supervised learning procedure to train models when few annotated images are available. In order to facilitate the dissemination of our method, we have implemented it as an open-source tool called ATLASS. Finally, we have evaluated our method with two benchmarks of biomedical image classification datasets.

RESULTS

Our method has been thoroughly tested both with small datasets and partially annotated biomedical datasets; and, it outperforms, both in terms of speed and accuracy, the existing AutoML tools when working with small datasets; and, might improve the accuracy of models up to a 10% when working with partially annotated datasets.

CONCLUSIONS

The work presented in this paper allows the use of deep learning techniques to solve an image classification problem with few resources. Namely, it is possible to train deep models with small, and partially annotated datasets of images. In addition, we have proven that our AutoML method outperforms other AutoML tools both in terms of accuracy and speed when working with small datasets.

Distributed Deep Features Extraction Model for Air Quality Forecasting

Several studies in environmental engineering emphasize the importance of air quality forecasting for sustainable development around the world. In this paper, we studied a new approach for air quality forecasting in Busan metropolitan city. We proposed a convolutional Bi-Directional Long-Short Term Memory (Bi-LSTM) autoencoder model trained using a distributed architecture to predict the concentration of the air quality particles (PM2.5 and PM10). The proposed deep learning model can automatically learn the intrinsic correlation among the pollutants in different location. Also, the meteorological and the pollution gas information at each location are fully utilized, which is beneficial for the performance of the model. We used multiple one-dimension convolutional neural network (CNN) layers to extract the local spatial features and a stacked Bi-LSTM layer to learn the spatiotemporal correlation of air quality particles. In addition, we used a stacked deep autoencoder to encode the essential transformation patterns of the pollution gas and the meteorological data, since they are very important for providing useful information that can significantly improve the prediction of the air quality particles. Finally, in order to reduce the training time and the resource consumption, we used a distributed deep leaning approach called data parallelism, which has never been used to tackle the problem of air quality forecasting. We evaluated our approach with extensive experiments based on the data collected in Busan metropolitan city. The results reveal the superiority of our framework over ten baseline models and display how the distributed deep learning model can significantly improve the training time and even the prediction accuracy.

A bird's-eye view of deep learning in bioimage analysis

Deep learning of artificial neural networks has become the de facto standard approach to solving data analysis problems in virtually all fields of science and engineering. Also in biology and medicine, deep learning technologies are fundamentally transforming how we acquire, process, analyze, and interpret data, with potentially far-reaching consequences for healthcare. In this mini-review, we take a bird's-eye view at the past, present, and future developments of deep learning, starting from science at large, to biomedical imaging, and bioimage analysis in particular.

Surgeon-robot interface development framework

The progress of robotic medicine leads to the emergence of an increasing number of highly specialized automated systems based on specialized software. In any such system, there is the task of translating the surgeon's requests into the process of automated procedure execution. The hardware and software system that provides the translation is the interface between the surgeon and the robot. This paper proposes a generalized framework architecture for the development of such software - the surgeon-robot interface. Existing implementations of such an interface are considered, solutions for the internal structure design of the framework are proposed. Experiments were performed using a prototype of the proposed framework. Such a development framework will allow one to effectively implement the surgeon-robot interfaces at all stages of the robotization of medical procedures, from prototype to final use in the operating room.