With Machine Learning and Deep Learning methods in arivis Vision4D segmentation of multi-channel images becomes a quick and easy task. No need to be an expert in bioinformatics: with your scientific expertise you mark and classify structures of interest in your samples and let the cloud train your neural network. Your benefit: you get reliable results in hours rather than weeks or even months of extensive manual work.
A conventional algorithm is designed by a specialist to answer exactly one question. In contrast, a Machine Learning algorithm can be adapted to a wide variety of questions, simply by training it. The Machine Learning algorithm “learns” patterns and adapts itself.
Machine Learning allows to use this expert knowledge of the user by drawing and classifying some samples of structures of interest into the image. The subsequent automatic training uses this information to automatically create the algorithm to be used to find these structures all over this and other images.
Our new UI and the smooth workflow integration guides the customer in a few steps through the process:
This tutorial demonstrates the workflow for deep learning applications with APEER, ZEN Intellesis and arivis Vision4D. Vision4D 3.6 fully supports import of deep learning models in the Open Neural Network Exchange (ONNX) format as well as the CZ model from ZEISS ZEN Intellesis and the APEER cloud-based image processing platform. With APEER you easily annotate and train new models or combine already existing ones into customized workflows, without the need for programming knowledge. Vision4D now gives you the flexibility to import and apply fully trained neural networks from various libraries and backends to your analysis pipelines to enable deep learning for automated analysis of your imaging data.
Hippocampus tissue section, transmission electron microscopy. In total, 30 TEM serial sections were used with 309 mitochondria objects, annotated manually with Vision4D 3.6. This manual annotation was used to train an ONNX U-Net Deep Learning model that was then applied on the whole dataset in Vision4D 3.6 for automated segmentation. In a following step, we calculated the ratio of the mean intensity of each object to its volume. This radiometric function reflects the differences in the mitochondria phenotype. These differences are visualized as a color-coded classification of the objects. Original imaging data was kindly provided by Dr. Wendy Bautista, MD PhD, Barrow Neurological Institute, Phoenix Children’s Hospital.
Machine Learning in arivis Vision4D is a fully integrated solution which allows to combine the segmentation results with any other functionality of the pipeline.
arivis Machine Learning works for several different multi-dimensional images from many modalities in microscopy:
The arivis Imaging Platform is a flexible computing universe for Imaging Science that scales, parallelizes, integrates and connects all imaging workflows, sparking organization-wide image data proficiency and efficiency at all levels. The integrated toolsets take care of everything from the file storage format to user and project-specific computations to reporting. The computational and management hubs that comprise the platform connect your datasets and take care of your central imaging databases and can expose data assets - including raw data and specified portions of raw data - to Machine Learning and AI routines.
Your modular software platform for extracting results from scientific images. Adjusts to your hardware for maximum power and smooth interactivity even with large image datasets of virtually unlimited size. Bring diverse tools into one environment and enable your users to connect them into productive workflows. Highly interactive for optimization and quality at every step. Extend Vision4D directly via Python and connect it to other applications via libraries.VisionVR Display real image data in Virtual Reality by utilizing patent-pending direct volume rendering techniques with no need to convert data or create surface models. Directly use your hands to move, rotate, scale, and shape your digital image data. Interactively proofread, edit, track or segment multi-dimensional images from nearly any source instrument. Discuss your findings and results worldwide in a collaborative connected environment.