UCL Bioimage Analysis Interest Group

The UCL Bioimage Analysis Interest Group aims to connect users and experts from different backgrounds who are interested in biological and biomedical image analysis. We hold monthly virtual meetings on the Zoom platform every last Friday of the month at 1-2pm. We host two speakers for short (15 min) and informal presentations each time, allowing plenty of time for discussion. Presentations are aimed at a broad audience and cover both new image analysis pipelines/tools and image analysis challenges people would like feedback on. We welcome work-in-progress presentations and highly encourage the participation of early-career researchers.

Image of mouse liver organoid analysed using Epitools, TissueAnalyser and Fiji. Credits: Alejandra Guzman Herrera, Mao Lab

Cells of a Drosophila wing disc segmented using plant-seg and Matlab. Credits: Pablo Vicente Munuera and Ricardo Barrientos, Mao Lab

Cells detected and brain regions segmented by cellfinder (Adam Tyson, https://cellfinder.info) from a whole mouse brain serial two-photon image. Data courtesy of Sepiedeh Keshavarzi and Chryssanthi Tsitoura

When: Last Friday of the month, 1-2pm

Zoom: https://ucl.zoom.us/j/98214347242?pwd=OXZwYmJlc3RTZi9IeG9VZjRWNjA3Zz09

Meeting ID: 982 1434 7242

Passcode: 952497

Upcoming meetings

31 March 2023 |

Kimberly Meechan (British Museum) - MoBIE: a Fiji plugin for sharing cloud-hosted big image data
Charlie Barker (UCL Cancer Institute) - Phenotype specific networks from 'omics' data

Join the #bioimage-analysis Slack channel here.

If you’d like to be added to the mailing list or are thinking of giving a presentation at the Interest Group, get in touch with Giulia Paci, Alessandro Felder, Pablo Vicente Munuera or Jonas Hartmann.

Past meetings

24 Sept 2021 |
Dale Moulding (ICH Confocal Microscopy Facility) - Surface Peeler: High speed 3D surface extraction with Fiji
Hernando Martinez Vergara (Stephenson-Jones group, Sainsbury Wellcome Centre) - Whole-body integration of gene expression and single-cell morphology

29 October 2021 |
Elisabeth Kugler (MacDonald group - UCL Institute of Ophtalmology) - GliaMorph: A data analysis toolkit to quantify glia cell morphology
Benjamin Blundell (Ch’ng group - King’s College London) - 3D Structure from 2D Microscopy Images using Deep-Learning

26 November 2021 |
Claire Walsh (CABI / UCL Mechanical Engineering) - Interdisciplinary collaboration on big image data sets
Stefania Marcotti (King’s College, Stramer group) - A workflow for rapid unbiased quantification of fibrillar feature alignment in biological images

28 January 2022 |
Nathan Day (UCL Lowe/Charras groups) - How does cell competition play out on a single-cell level?
Rocco d’Antuono (Crick Advanced Light Microscopy STP) - ZELDA: A 3D Image Segmentation and Parent-Child Relation Plugin for Microscopy Image Analysis in napari

25 February 2022 |
Dan Tudosiu (King’s College - Cardoso group) - SynthAnato: Towards Morphologically Correct Synthetic Brain Images
Lucinda Evans (Royal Veterinary College - Pitsillides group) - Using high-resolution synchrotron imaging to resolve new detail and identify potential osteoarthritis biomarkers in mouse knee joints

29 April 2022 |
Hugh Ford (LMCB - Chubb group) - Using image analysis to extract the physics of cell aggregation and swarming
Jessica Forsyth (University of Manchester - Plusa & Cotter group) - IVEN: A quantitative tool to describe 3D cell position and neighbourhood

27 May 2022 |
Soham Mandal (EBI - Uhlmann group) - Splinedist: Automated Cell Segmentation With Spline Curves
Kasra Hosseini & Evangeline Corcoran (The Alan Turing Institute) - Automated plant phenotyping: plant patch classification with MapReader

16-17 June 2022 |
Special event - UCL Bioimage Analysis Group Collaborative Workshop
Full information and registration details here.

24 June 2022 |
Special event - joint meeting with UCL Bioimaging Interest Group
Paul Frankel, Isabelle Bond (UCL Institute of Cardiovascular Science) - The (virtual) reality of analysing zebrafish vasculature: Microscopy, registration, and quantification.

30 September 2022 |
David Barry (Crick Advanced Light Microscopy STP) – “How to be a Core Facility Image Analyst”
Pablo Vicente Munuera (LMCB, Mao group) – “Workshop on 3D segmentation: Cellpose + trackmate”

28 October 2022 |
Paddy Roddy (UCL ARC) – My Experiences with Neuroglancer - a 3D Web Based Viewer in the Cloud
Tchern Lenn (UCL Cancer Institute) – Why and how I used a UCL HPC cluster to analyse multi-colour 3D time-series

25 November 2022 |
Namid Stillman (UCL CDB - Mayor lab) - Connecting the dots of cell migration: using generative models to couple biophysics to data
Wolfram Pönisch (Cambridge - Paluch lab) - How to quantify the stochastic dynamics of cell shape during cell state transitions

27 January 2023 |
Megan Joseph (LCN, Simonelli Lab) - Quantitative Super Resolution Image Analysis
Aoife Hughes (The Alan Turing Institute) - Title TBC