22 papers · ranked by Valyu relevance
Thomas Bartz–Beielstein
The goal of hyperparameter tuning (or hyperparameter optimization) is to optimize the hyperparameters to improve the performance of the machine or deep learning model. spotPython ("Sequential Parameter Optimization Toolbox in Python") is the Python version of the well-known hyperparameter tuner SPOT, which has been…
Thomas Bartz–Beielstein
- If DEVICE is set to "auto" or None, spotPython will automatically select the device. - – This might result in "mps" on Macs, which is not the best choice for simple neural nets. 1 Alternatively, the source code can be downloaded from gitHub: https://github.com/sequential-parameteroptimization/spotPython. 2 We were…
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…
Yifan Li, Xinyu Zhou, Yunhao Ge, Yu Kong
Robotic manipulation is often specified through language instructions or task identifiers, yet cluttered environments with similar objects are better handled by spatially indicating what to move and where to place it. Addressing the vision-centric challenge of object and goal specification, we present, to the best of…
Talaya Farasat, Atiqullah Ahmadzai, Aleena Elsa George, Sayed Alisina Qaderi + 2 more
Vulnerability Detection in Python Authors: ['Talaya Farasat' 'Atiqullah Ahmadzai' 'Aleena Elsa George' 'Sayed Alisina Qaderi' 'Danilo Dordevic' 'Joachim Posegga'] Software vulnerabilities are a fundamental cause of cyber attacks. Effectively identifying these vulnerabilities is essential for robust cybersecurity, yet…
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…
Talaya Farasat, Joachim Posegga
Detection Authors: ['Talaya Farasat' 'Joachim Posegga'] Software vulnerabilities are a fundamental reason for the prevalence of cyber attacks and their identification is a crucial yet challenging problem in cyber security. In this paper, we apply and compare different machine learning algorithms for source code…
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…
Dimitar Georgiev, Simon Vilms Pedersen, Ruoxiao Xie, Álvaro Fernández-Galiana + 2 more
Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still impeded by the lack of software, methodological and data standardisation, and the…
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…
Hamed Tahmooresi, Abbas Heydarnoori, Alireza Aghamohammadi
—Python is a popular, widely used, and general-purpose programming language. In spite of its ever-growing community, researchers have not performed much analysis on Python's topics, trends, and technologies which provides insights for developers about Python community trends and main issues. In this article, we examine…
Authors not listed
With the rapid growth of chemical data and information, there is an increasing need for chemistry undergraduates to master Python tools for analyzing large chemical datasets and extracting key or feature information. Currently, more than 100,000 types of metal-organic frameworks (MOFs), as the material recently awarded…
Martin Seifrid, Felix Strieth-Kalthoff, Mohammad Haddadnia, Tony Wu + 7 more
We introduce Chemspyd, a lightweight, open-source Python package for operating the popular laboratory robotic platforms from Chemspeed Technologies. As an add-on to the existing proprietary software suite, Chemspyd enables dynamic communication with the automated platform, laying the foundation for its modular…
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…