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Alex Henderson

@alexhenderson.info

Open Research Fellow at University of Manchester, UK (he/him). chemometrics | research data management | linked data https://alexhenderson.info

46 Posts306 Follower587 Folgt
Alex Henderson@alexhenderson.info · 2mo ago

"Application of a Hopfield neural network to extract essential spectral patterns from ToF–SIMS spectra of peptides" ANAL. SCI. 42, 589–598 (2026). doi.org/10.1007/s442...

Application of a Hopfield neural network to extract essential spectral patterns from ToF–SIMS spectra of peptides - Analytical Sciences

A recurrent neural network (RNN) system based on a Hopfield neural network (HNN) was developed to extract essential spectral patterns from the time-of-flight secondary ion mass spectrometry (ToF–SIMS) spectra of peptide samples. Because ToF–SIMS produces various fragment ions from organic molecules, the interpretation of ToF–SIMS spectra is generally complicated. ToF–SIMS is useful for peptide analysis because it detects specific amino acid fragment ions from peptides that indicate peptide information. However, the ToF–SIMS spectra also contain fragment ions that do not preserve the main structures of the original molecules, which makes them difficult to interpret. Therefore, it is crucial to extract essential spectral patterns from the ToF–SIMS spectra of organic materials. Peptides were selected as the target organic materials for this study due to their systematic chemical structures. A modified HNN was trained on the ToF–SIMS spectra of each peptide, and the trained HNNs were then used to recall patterns for various peptide ToF–SIMS spectra. The results show that the modified HNN recall essential spectra containing specific ions, including the protonated molecular ions and amino acid fragment ions of target peptides. Furthermore, the HNN results revealed differences and similarities between peptides with similar and different amino acid sequences. Thus, this study demonstrates the effectiveness of the HNN in interpreting complex spectra and its potential for preprocessing data for further analysis. Graphical abstract

doi.org

NFDI4Chem@nfdi4chem.de · 3mo ago

Not sure where to publish your data? Meet the Repositories brings together chemistry-friendly repositories to discuss scope, use cases & FAIR data publishing. Find the right home for your research data—and ask repository experts directly. 🧪 30.06.2026, 10-12 am https://t1p.de/jpjfc #OpenScience

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Jon Lim, FRCP PhD@drjonlim.bsky.social · 3mo ago

Featured on BBC News: #TeamManchester is growing. 🚀 Cancer Research UK Manchester Institute will be receiving an extra £6m a year in investment, creating 8️⃣ senior research roles: 4 group leaders, 2 senior group leaders & 2 clinician scientists. @cruk-mi.bsky.social www.bbc.co.uk/news/article...

Manchester cancer research lab's £6m extra annual cash boost

Cancer Research UK Manchester Institute says the extra cash will make a "huge difference" to its work.

bbc.co.uk

Alex Henderson@alexhenderson.info · 4mo ago

AirNet: A Deep Learning-Driven Auto Baseline Correction Algorithm Balancing Global Smoothness and Local Fidelity Anal. Chem. 2026 doi.org/10.1021/acs.... #raman

AirNet: A Deep Learning-Driven Auto Baseline Correction Algorithm Balancing Global Smoothness and Local Fidelity

Baseline correction is a critical preprocessing step to eliminate non-Raman scattering backgrounds in the Raman/SERS spectrum, ensuring accurate peak positions and intensities for qualitative and quan...

pubs.acs.org

Alex Henderson@alexhenderson.info · 4mo ago

"Conceptual Differences Between Hyperspectral Unmixing, PCA, and Clustering: A Practical Demonstration Using Single-Cell Raman Imaging" Journal of Chemometrics 40, no. 6 (2026): e70152 doi.org/10.1002/cem.... #shortcommunication

Conceptual Differences Between Hyperspectral Unmixing, PCA, and Clustering: A Practical Demonstration Using Single‐Cell Raman Imaging

Hyperspectral unmixing is a well-established approach for analyzing spectroscopic images by recovering chemically interpretable component spectra and their spatial distributions. Despite its distinct...

doi.org

Kevin Thiessen, PhD@kevinthiessen.bsky.social · 6mo ago

This particularly becomes an issue w/ Red-Green LUTs. You can easily make the switch using this FIJI Plugin: In FIJI > Color > Replace Red with Magenta. This can be applied to videos as well. You can also view how images may appear to those w/ vision impairments: > Color > Simulate Color Blindness

Screenshot of a slide from a journal club presentation. You can see an image of a clown and a figure as they appear to people with normal vision, which appear very dim to people with protanopia. When you replace red with magenta using FIJI, the images appear much more clear for people with red color blindness.
PLOS@plos.org · 7mo ago

@plosbiology.org is formalizing its long‑standing practice of asking authors to share research code, introducing a mandatory #code‑sharing policy and clarifying what is meant by code sharing. Learn more and find guidance on best practice: plos.io/4reyX3v

PLOS Biology@plosbiology.org · 7mo ago

In support of #OpenScience, we routinely ask authors to openly share their #research #code before publication. We are now formalizing this practice with a mandatory #code-sharing policy and clarifying what we mean by code sharing. May be nice to cut-out the box for reference plos.io/47dPeOW 🧪

Specific details about PLOS Biology's mandatory code-sharing policy
PLOS Biology@plosbiology.org · 7mo ago

In support of #OpenScience, we routinely ask authors to openly share their #research #code before publication. We are now formalizing this practice with a mandatory #CodeSharing policy and clarifying what we mean by code sharing.

Formalizing our commitment to code sharing

In support of open science, PLOS Biology routinely asks authors to openly share their research code before publication. We are now formalizing this practice with a mandatory code sharing policy and…

plos.io

Accessibility Awareness@a11yawareness.bsky.social · 10mo ago

Many struggle with writing alt text for charts and other other data visualizations. Amy Cesal's "Writing Alt Text for Data Visualization" hammers home the importance of explaining the chart type, the type of data, and the reason for the chart. medium.com/nightingale/...

Writing Alt Text for Data Visualization

How do you write text that conveys the whole meaning of a visualization? You probably can’t. But that doesn’t mean that you shouldn’t try

medium.com

Alex Henderson@alexhenderson.info · 11mo ago

[from DiceResearch on X] "OWLAPY: A Pythonic Framework for OWL Ontology Engineering" 👉Check it out: arxiv.org/abs/2511.08232 🔎 OWLAPY is a comprehensive Python framework for OWL ontology engineering, already over 50k downloads!

OWLAPY: A Pythonic Framework for OWL Ontology Engineering

In this paper, we introduce OWLAPY, a comprehensive Python framework for OWL ontology engineering. OWLAPY streamlines the creation, modification, and serialization of OWL 2 ontologies. It uniquely int...

arxiv.org

Carlo Lepelaars@carlolepelaars.bsky.social · 2y ago

Struggling with Python `re`? regex is a superset of re with additional functionality and more thorough Unicode support. It is very powerful and still kind of an open secret. When I saw @howard.fm explain this I just had to write about it! Today I Learned: carlo.ai/til/regex-se...

regex.search - Carlo Lepelaars

Using regex.search for simple string parsing. `regex` is a superset of `re` with additional functionality and more thorough Unicode support.

carlo.ai

Alex Henderson@alexhenderson.info · 12mo ago

📢 New job positions in Heath Informatics @manchester.ac.uk www.jobs.manchester.ac.uk/Job/JobDetai... Lots of RO-Crate, #metadata, #FAIR and you get to join the excellent eScience Lab team!

Research Fellow (Health Informatics):Oxford Road

Join our world-leading group, the eScience Lab (esciencelab.org.uk) at The University of Manchester, where innovation meets impact in data-driven life science research. We are seeking a talented and motivated Research Fellow to lead work within the TREvolution project—an exciting DARE UK initiative focused on advancing Trusted Research Environments (TREs) for multi-site, AI-enabled health data analytics.

jobs.manchester.ac.uk

@jofmicroscopy.bsky.social · 12mo ago

🔬New Methods and Protocols published! The authors present a methodology for deep learning-based segmentation by transforming high-quality ex situ laboratory data to train models for segmentation of in situ synchrotron data, demonstrated through a metal oxide dissolution study.

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