13 papers · ranked by Valyu relevance
Francesco Padovani, Ivana Čavka, Ana Rita Rodrigues Neves, Cristina Piñeiro López + 9 more
The analysis of spot-like structures is a widespread task in microscopy-based cell biology. Existing solutions are typically specific to single applications and do not use multi-dimensional information from 5D datasets. Therefore, experimental scientists often resort to subjective manual annotation. Here, we present…
Xingyi Chen, Michael Totty, Stephanie C. Hicks
Spatially-resolved transcriptomics (SRT) generates large and heterogeneous datasets where global (tissue-wide) quality control (QC) metrics often over-aggressively remove biologically meaningful regions or miss localized artifacts. Recently, spatially-aware QC metrics have been introduced in SpotSweeper, but this is…
Jinpu Li, Mauminah Raina, Yiqing Wang, Chunhui Xu + 7 more
Emerging spatial omics technologies empower comprehensive exploration of biological systems from multi-omics perspectives in their native tissue location in two and three- dimensional space. However, sparse sequencing capacity and growing spatial resolution in spatial omics present significant computational challenges…
Emily Laubscher, Xuefei (Julie) Wang, Nitzan Razin, Tom Dougherty + 7 more
Image-based spatial transcriptomics methods enable transcriptome-scale gene expression measurements with spatial information but require complex, manually-tuned analysis pipelines. We present Polaris, an analysis pipeline for image-based spatial transcriptomics that combines deep learning models for cell segmentation…
Stavros P. Hadjisolomou, George El-Haddad
Coleoid cephalopods (squid, octopus, and sepia) are renowned for their elaborate body patterning capabilities, which are employed for camouflage or communication. The specific chromatic appearance of a cephalopod, at any given moment, is a direct result of the combined action of their intradermal pigmented…
Zijian Niu, Aoife O’Farrell, Jingxin Li, Sam Reffsin + 4 more
Single-molecule RNA fluorescence in situ hybridization (RNA FISH)-based spatial transcriptomics methods have enabled the accurate quantification of gene expression at single-cell resolution by visualizing transcripts as diffraction-limited spots. While these methods generally scale to large samples, image analysis…
Albert Dominguez Mantes, Antonio Herrera, Irina Khven, Anjalie Schlaeppi + 6 more
The identification of spot-like structures in large and noisy microscopy images is an important task in many life science techniques, and it is essential to their quantitative performance. For example, imaging-based spatial transcriptomics (iST) methods rely critically on the accurate detection of millions of…
Zhiyou Wang, Xiaoqing Huang, Zhiqiang Cheng
An automatic spot identification method is developed for high throughput surface plasmon resonance imaging (SPRi) analysis. As a combination of video accessing, image enhancement, image processing and parallel processing techniques, the method can identify the spots in SPRi images of the microarray from SPRi video…
Emmanuel Bouilhol, Anca F. Savulescu, Edgar Lefevre, Benjamin Dartigues + 2 more
'Benjamin Dartigues' 'Robyn Brackin' 'Macha Nikolski'] Detection of RNA spots in single-molecule fluorescence in-situ hybridization microscopy images remains a difficult task, especially when applied to large volumes of data. The variable intensity of RNA spots combined with the high noise level of the images often…
Vasudha Jha, Robert H. Cudmore
Brightest path tracing is a widely used image processing technique in several fields including biology, geography, and geology. However, despite the availability of many image processing libraries in Python, few offer an out-of-the-box implementation of a bright-est path tracing algorithm. This paper presents a Python…
Damir Krstinić, Ana Kuzmanić Skelin, Ivan Milatić
Laser pointers are one of the most widely used interactive and pointing devices in different human-computer interaction systems. Existing approaches to vision-based laser spot tracking are designed for controlled indoor environments with the main assumption that the laser spot is very bright, if not the brightest, spot…
Lingjiang Li, Maolin Li, Weijun Sun, Zhenni Li + 2 more
'Shah Nawaz Burokur'] Spot detection has attracted continuous attention for laser sensors with applications in communication, measurement, etc. The existing methods often directly perform binarization processing on the original spot image. They suffer from the interference of the background light. To reduce this kind…
Mario M. Krell, Sirko Straube, Anett Seeland, Hendrik Wöhrle + 4 more
'Johannes Teiwes' 'Jan H. Metzen' 'Elsa A. Kirchner' 'Frank Kirchner'] In neuroscience large amounts of data are recorded to provide insights into cerebral information processing and function. The successful extraction of the relevant signals becomes more and more challenging due to increasing complexities in…