We provide notes on how to use a graphical user interface (GUI), implemented with MATLAB, for aligning imaging datasets of biological tissue. The original use was for matching two imaging data sets, where one set was taken of the living preparation and another was taken post-fixation and following immunohistochemical processing. This technique is described in detail in an accompanying paper (Parrish et al., [1], where we also include information about the experimental procedures, and examples of the usage of the GUI.
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http://dx.doi.org/10.1016/j.dib.2018.07.069 | DOI Listing |
J Chem Inf Model
January 2025
Analytical Research & Development, MRL, Merck & Co., Inc., Rahway, New Jersey 07065, United States.
The screening of chemical libraries is an essential starting point in the drug discovery process. While some researchers desire a more thorough screening of drug targets against a narrower scope of molecules, it is not uncommon for diverse screening sets to be favored during the early stages of drug discovery. However, a cost burden is associated with the screening of molecules, with potential drawbacks if particular areas of chemical space are needlessly overrepresented.
View Article and Find Full Text PDFJ Proteome Res
January 2025
Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen 72074, Germany.
Liquid chromatography-mass spectrometry (LC-MS) is an indispensable analytical technique in proteomics, metabolomics, and other life sciences. While OpenMS provides advanced open-source software for MS data analysis, its complexity can be challenging for nonexperts. To address this, we have developed OpenMS WebApps, a framework for creating user-friendly MS web applications based on the Streamlit Python package.
View Article and Find Full Text PDFPLoS Biol
January 2025
School of Biosciences and Bateson Centre, University of Sheffield, Western Bank, Sheffield, United Kingdom.
Heart development involves the complex structural remodelling of a linear heart tube into an asymmetrically looped and ballooned organ. Previous studies have associated regional expansion of extracellular matrix (ECM) space with tissue morphogenesis during development. We have developed morphoHeart, a 3D tissue segmentation and morphometry software with a user-friendly graphical interface (GUI) that delivers the first integrated 3D visualisation and multiparametric analysis of both heart and ECM morphology in live embryos.
View Article and Find Full Text PDFNano Lett
January 2025
Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Tomtebodavägen 23, 17165 Solna, Sweden.
Single particle profiling (SPP) is a unique methodology to study nanoscale bioparticles such as liposomes, lipid nanoparticles, extracellular vesicles, and lipoproteins in a single particle and high throughput manner. The initial version requires the single photon counting modules for data acquisition, which limits its adoptability. Here, we present imaging-based SPP (iSPP) that can be performed by imaging a spot over time in the common imaging mode with confocal detectors.
View Article and Find Full Text PDFBMC Bioinformatics
January 2025
Biology Department, University of Massachusetts Amherst, Amherst, MA, USA.
Background: High-throughput behavioral analysis is important for drug discovery, toxicological studies, and the modeling of neurological disorders such as autism and epilepsy. Zebrafish embryos and larvae are ideal for such applications because they are spawned in large clutches, develop rapidly, feature a relatively simple nervous system, and have orthologs to many human disease genes. However, existing software for video-based behavioral analysis can be incompatible with recordings that contain dynamic backgrounds or foreign objects, lack support for multiwell formats, require expensive hardware, and/or demand considerable programming expertise.
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