Spatial transcriptomics is a cutting-edge technique that combines gene expression with spatial information, allowing researchers to study molecular patterns within tissue architecture. Here, we present IAMSAM, a user-friendly web-based tool for analyzing spatial transcriptomics data focusing on morphological features. IAMSAM accurately segments tissue images using the Segment Anything Model, allowing for the semi-automatic selection of regions of interest based on morphological signatures. Furthermore, IAMSAM provides downstream analysis, such as identifying differentially expressed genes, enrichment analysis, and cell type prediction within the selected regions. With its simple interface, IAMSAM empowers researchers to explore and interpret heterogeneous tissues in a streamlined manner.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11552325 | PMC |
| http://dx.doi.org/10.1186/s13059-024-03380-x | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Attention-guided convolutional network for bias-mitigated and interpretable oral lesion classification.
Sci Rep
December 2024
Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Canada.
Accurate diagnosis of oral lesions, early indicators of oral cancer, is a complex clinical challenge. Recent advances in deep learning have demonstrated potential in supporting clinical decisions. This paper introduces a deep learning model for classifying oral lesions, focusing on accuracy, interpretability, and reducing dataset bias.
View Article and Find Full Text PDFAutomatic detection and multi-component segmentation of brain metastases in longitudinal MRI.
Sci Rep
December 2024
Institute of Informatics, HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland, Sierre, Switzerland.
Manual segmentation of lesions, required for radiotherapy planning and follow-up, is time-consuming and error-prone. Automatic detection and segmentation can assist radiologists in these tasks. This work explores the automated detection and segmentation of brain metastases (BMs) in longitudinal MRIs.
View Article and Find Full Text PDFA deep transfer learning based convolution neural network framework for air temperature classification using human clothing images.
Sci Rep
December 2024
Department of Electrical Engineering, College of Engineering, Taif University, P.O. BOX 11099, 21944, Taif, Saudi Arabia.
Weather recognition is crucial due to its significant impact on various aspects of daily life, such as weather prediction, environmental monitoring, tourism, and energy production. Several studies have already conducted research on image-based weather recognition. However, previous studies have addressed few types of weather phenomena recognition from images with insufficient accuracy.
View Article and Find Full Text PDFPseudolabel guided pixels contrast for domain adaptive semantic segmentation.
Sci Rep
December 2024
The Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, 200237, China.
Semantic segmentation is essential for comprehending images, but the process necessitates a substantial amount of detailed annotations at the pixel level. Acquiring such annotations can be costly in the real-world. Unsupervised domain adaptation (UDA) for semantic segmentation is a technique that uses virtual data with labels to train a model and adapts it to real data without labels.
View Article and Find Full Text PDFChanges in Disc Status and Condylar Regeneration After Intracapsular Condylar Fractures in Rabbits.
Oral Dis
December 2024
Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.
Background: The treatment procedure for intracapsular condylar fractures (ICF) is still being debated. The temporomandibular joint (TMJ) disc is a key factor for treating ICF. The study aims to investigate the changes in TMJ disc status and condylar cartilage regeneration following ICF in a rabbit model, to assist in planning treatment.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!