4 research outputs found
[Work in progress] Scalable, out-of-the box segmentation of individual particles from mineral samples acquired with micro CT
Minerals are indispensable for a functioning modern society. Yet, their
supply is limited causing a need for optimizing their exploration and
extraction both from ores and recyclable materials. Typically, these processes
must be meticulously adapted to the precise properties of the processed
particles, an extensive characterization of their shapes, appearances as well
as the overall material composition. Current approaches perform this analysis
based on bulk segmentation and characterization of particles imaged with a
micro CT, and rely on rudimentary postprocessing techniques to separate
touching particles. However, due to their inability to reliably perform this
separation as well as the need to retrain or reconfigure methods for each new
image, these approaches leave untapped potential to be leveraged. Here, we
propose ParticleSeg3D, an instance segmentation method that is able to extract
individual particles from large micro CT images taken from mineral samples
embedded in an epoxy matrix. Our approach is based on the powerful nnU-Net
framework, introduces a particle size normalization, makes use of a border-core
representation to enable instance segmentation and is trained with a large
dataset containing particles of numerous different materials and minerals. We
demonstrate that ParticleSeg3D can be applied out-of-the box to a large variety
of particle types, including materials and appearances that have not been part
of the training set. Thus, no further manual annotations and retraining are
required when applying the method to new mineral samples, enabling
substantially higher scalability of experiments than existing methods. Our code
and dataset are made publicly available
Genomics, Proteomics, and Metabolomics Approaches to Improve Abiotic Stress Tolerance in Tomato Plant
To explore changes in proteins and metabolites under stress circumstances, genomics, proteomics, and metabolomics methods are used. In-depth research over the previous ten years has gradually revealed the fundamental processes of plants’ responses to environmental stress. Abiotic stresses, which include temperature extremes, water scarcity, and metal toxicity brought on by human activity and urbanization, are a major cause for concern, since they can result in unsustainable warming trends and drastically lower crop yields. Furthermore, there is an emerging reliance on agrochemicals. Stress is responsible for physiological transformations such as the formation of reactive oxygen, stomatal opening and closure, cytosolic calcium ion concentrations, metabolite profiles and their dynamic changes, expression of stress-responsive genes, activation of potassium channels, etc. Research regarding abiotic stresses is lacking because defense feedbacks to abiotic factors necessitate regulating the changes that activate multiple genes and pathways that are not properly explored. It is clear from the involvement of these genes that plant stress response and adaptation are complicated processes. Targeting the multigenicity of plant abiotic stress responses caused by genomic sequences, transcripts, protein organization and interactions, stress-specific and cellular transcriptome collections, and mutant screens can be the first step in an integrative approach. Therefore, in this review, we focused on the genomes, proteomics, and metabolomics of tomatoes under abiotic stress
Data: Particle dispersions 3D characterization of chromite ore particles with different sizes
Particle dispersions for 3D analysis using computed tomography prepared according to a standardized sample preparation procedure.
Particles are from a Chromite ore (Kemi mine). Each sample has a specific size class.
Analysis of the data a published open sourc