Are you planning to publish a paper involving microscopy ?
You have the possibility to contact the microscopists and/or image analysts in our facility.
The BIOP staff is happy to guide you into following the FAIR principles and provide feedback about your Image Acquisition, Processing, Analysis and Visualization.
Furthermore the BIOP staff can :
- Assist in the production of Materials and Methods sections regarding microscopy and image processing.
- Advise on data and code accessibility and sharing.
- Provide feedback on best practices for data visualization.
- Advise on how to share data and code online ( Copyrighting, licensing, uploading ).
Moreover, this provides the BIOP with useful insights how its tools and services have contributed to the scientific literature.
How to acknowledge the BIOP in a publication?
The type of acknowledgement depends on the type of work and collaboration we have undertaken. For publications the rules and recommendations layed out in the EPFL compliance guide apply.
For contributions to a publication which do not fulfill the criteria above, we recommend the following sentence:
We would like to thank the EPFL BioImaging & Optics Core Facility and in particular [person(s)] for their assistance in [imaging / image processing].
It has been reported recently [1] that imaging methods are often not properly documented in publications.
In case you have a general question regarding Image acquisition, processing, analysis and visualization, or are unsure what to include into your Materials and Methods section, do not hesitate to drop us a line or pass by. We are happy to:
- Assist in the production of Materials and Methods sections regarding microscopy and image processing.
- Advise on data and code accessibility and sharing.
- Provide feedback on best practices for data visualization.
- Advise on how to share data and code online ( Copyrighting, licensing, uploading ).
[1] Marqués et al.: Science Forum: Imaging methods are vastly underreported in biomedical research, eLife 2020;9:e55133, doi: 10.7554/eLife.55133, Aug 11, 2020.
Selected Examples
Latest Publications
Below you will find recent publications by all members of the BioImaging & Optics Platform.
To find all publications, you may head to InfoScience.
2026
A Single-organoid Workflow for quantitative Imaging classiFication and Tracking (SWIFT)
Communications biology. 2026. Vol. 9, num. 1. DOI : 10.1038/s42003-026-10768-x.Kidney-specific deletion of the BicC family RNA-binding protein 1 triggers an ADPKD-like cystogenic program
iScience. 2026. Vol. 29, num. 8, p. 117020. DOI : 10.1016/j.isci.2026.117020.DGAT1-mediated lipid droplet accumulation promotes M. bovis BCG persistence on dendritic cells by acting as an immunoinflammatory platform through PGE₂ signaling
Inflammation. 2026. DOI : 10.1007/s10753-026-02584-6.A Robust and Generalizable Low-Input Spatial Proteomics Workflow Enabling Deep Proteome Coverage
2026
Spatial architecture of tenascin-c–driven ECM–immune niches in sarcoma.
Journal of Clinical Oncology. 2026. Vol. 44, num. 16_suppl. DOI : 10.1200/jco.2026.44.16_suppl.e23562.Automated Renal Tubule and Cyst Quantification (ARTCyQ)
2026.2025
Unified mass imaging maps the lipidome of vertebrate development
Nature Methods. 2025. DOI : 10.1038/s41592-025-02771-7.Injury-induced intestinal stem cell renewal requires capillary morphogenesis gene 2
EMBO Molecular Medicine. 2025. DOI : 10.1038/s44321-025-00295-3.ABBA+BraiAn, an integrated suite for whole-brain mapping, reveals brain-wide differences in immediate-early genes induction upon learning
Cell Reports. 2025. Vol. 44, num. 7. DOI : 10.1016/j.celrep.2025.115876.Adaptive Optics-Transscleral Flood Illumination Imaging of Retinal Pigment Epithelium in Dry Age-Related Macular Degeneration
Cells. 2025. Vol. 14, num. 9. DOI : 10.3390/cells14090633.Development of image analysis tool to evaluate Langerhans cell migration after exposure to isothiazolinones
ARCHIVES OF TOXICOLOGY. 2025. DOI : 10.1007/s00204-025-04013-3.Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression
Nature Methods. 2025. DOI : 10.1038/s41592-025-02662-x.2024
Cell density quantification of high resolution Nissl images of the juvenile rat brain
Frontiers In Neuroanatomy. 2024. Vol. 18, p. 1463632. DOI : 10.3389/fnana.2024.1463632.High-resolution adaptive optics-trans-scleral flood illumination (AO-TFI) imaging of retinal pigment epithelium (RPE) in central serous chorioretinopathy (CSCR)
Scientific reports. 2024. Vol. 14, num. 1. DOI : 10.1038/s41598-024-64524-4.A multicellular developmental program in a close animal relative
Nature. 2024. Vol. 635, num. 8038, p. 382 – 389. DOI : 10.1038/s41586-024-08115-3.Structural and molecular characterization of astrocyte and vasculature connectivity in the mouse hippocampus and cortex
Glia. 2024. Vol. 72, num. 11, p. 2001 – 2021. DOI : 10.1002/glia.24594.Supplementary files for Machine learning for histological annotation and quantification of cortical layers
2024.Inhibition of CERS1 in skeletal muscle exacerbates age-related muscle dysfunction
eLife. 2024. Vol. 12. DOI : 10.7554/eLife.90522.3.Cellpose training data and scripts from “Inhibition of CERS1 in aging skeletal muscle exacerbates age-related muscle impairments”
2024.2023
Community-developed checklists for publishing images and image analyses
Nature Methods. 2023. DOI : 10.1038/s41592-023-01987-9.Conference Posters
You can find our conference posters here in PDF format