Reproducibility - FocalPlane

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From Click to Code: Reproducibility in Bio-image Analysis

Posted by Mara Lampert, on 5 August 2025

Reproducibility is at the heart of good science. But when it comes to bio-image analysis, it can feel difficult to achieve. Complex datasets, shifting software environments, and countless manual tweaks often make it hard to retrace your own steps and share workflows with others. An aim should be to package the entire analysis, like code, data

Bioimage Analysis: A Call for Standards and Community Accountability

Posted by Haydee Hernández, on 20 November 2024

Achieving true reproducibility in bioimage analysis is a milestone that may seem far away, but it is a goal to which we must aspire. The current reality is that many published papers lack the necessary documentation, and full disclosure of the steps they followed to obtain results, necessary to reproduce their methodologies accurately. This gap

FocalPlane features... reproducibility in imaging - recordings

Posted by FocalPlane, on 8 November 2024

For the October edition of FocalPlane features…, we hosted a webinar on reproducibility in imaging with talks from Helena Jambor and Kota Miura. Helena told us, ‘How not to lie with image data’ and focussed on data presentation. Helena also touched on the importance of accessibility when presenting data and much of the discussion following

FocalPlane features... reproducibility in imaging

Posted by FocalPlane, on 23 September 2024

Our next FocalPlane features… webinar is on reproducibility with talks from Helena Jambor and Kota Miura. Helena's talk will cover the community checklists for publishing images, which were developed by QUAREP-LiMi and published at the end of 2023, as she tells us 'How not to lie with image data'. Kota's talk will focus on bioimage analysis and

Image checklists v1.0 from QUAREP-LiMi

Posted by Helen Zenner, on 16 March 2023

QUAREP-LiMi (Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy) is a community group of light microscopists, science communicators, business representatives, vendors and application specialists aiming to improve both quality assessment and quality control in microscopy. QUAREP-LiMi is organised into (currently) 13 working groups, focusing on areas such as illumination power, lateral and

Managing Scientific Python environments using Conda, Mamba and friends

Posted by Robert Haase, on 8 December 2022

TL:DR: This blog post gives short instructions and explanations to demystify how some scientific Python programmers, including myself, organize their coding environment for the sake of reproducibility of science. We will see what conda and mamba are, what they are good for, and how to use them properly. We will also take a short excursion

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Microscopy-related articles from our journals

HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples Development 2024 151: dev202307
filoVision – using deep learning and tip markers to automate filopodia analysis J Cell Sci 2024 137: jcs261274
C omputational tools for quantifying actin filament numbers, lengths, and bundling Biology Open 2024 13: bio.060267

Microscopy-related preprint highlights

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