Below are ways to collaborate our lab, pointers to our software and its documentation, and the educational resources and papers we have been a part of. We hope these resources help you out!
This page last updated 2025-Feb-06
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Work with us | Software | Educational materials | Papers
CellProfiler annual support plan
Beth's Broad bio page with contact email
Google Summer of Code 2025 Project ideas
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CellProfiler | CellProfiler Analyst | Piximi | Distributed Something | Bilayers
papers - CellProfiler-plugins [2023] / CellProfiler 4 [2021] / CellProfiler 3 [2018]
papers - CellProfiler Analyst 3 [2021]
Distributed tools - Distributed-CellProfiler / Distributed-Collate / Distributed-DeepProfiler / Distributed-Fiji / Distributed-HelloWorld / Distributed-OMEZarrCreator
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Educational papers | Things we lead | Major contributors | Minor contributors
The Twenty Questions of Bioimage Object Analysis[2023] / Tool implementation
A biologist’s guide to planning and performing quantitative bioimaging experiments[2023]
A postdoctoral training program in bioimage analysis[2024]
Current lab preprints (from Beth's CV)
The Scientific Community Image Forum - Forum.image.sc / Paper - Scientific Community Image Forum: A discussion forum for scientific image software[2019]
Bioimaging Guide - English / Spanish / Portuguese / Czech
The Image Based Profiling Handbook
The Cell Painting Gallery (image repository) - AWS RODA Website / Explore on Quilt / Paper - Cell Painting Gallery: an open resource for image-based profiling[2024]
Global Bioimage Analysts' Society (GloBIAS) Global Registries - For bioimage analysts / For bioimage analysis trainers
Virtual I2K Meeting - 2023 edition / 2024 edition
Online guide for checklists for imaging and image analysis / Paper - Community-developed checklists for publishing images and image analysis [2023]
Metrics Reloaded online metric chooser / Paper 1 - Metrics reloaded: recommendations for image analysis validation[2024] / Paper 2 - Understanding metric-related pitfalls in image analysis validation[2024]
Microtutor imaging education platform
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Protocols | Reviews | Community Surveys | Opinions/Perspectives
ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis[2020]
Interpreting image-based profiles using Morpheus and single-cell visualization[2023]
Optimizing the Cell Painting assay for image-based profiling[2023]
Open-source deep-learning software for bioimage segmentation[2021]
Defining the boundaries: challenges and advances in identifying cells in microscopy images[2024]
2020 BioImage Analysis Survey: Community experiences and needs for the future[2021]
Bridging Imaging Users to Imaging Analysis - A community survey[2023]
Moving beyond the desktop: Prospects for Practical Bioimage Analysis via the Web[2023]
Building momentum through networks: Bioimaging across the Americas[2024]
The Crucial Role of BioImage Analysts in Scientific Research and Publication[2024]
A Call for FAIR and Open-Access Training Materials to advance Bioimage Analysis (preprint)[2024]
Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data (preprint)[2024]
Enabling Global Image Data Sharing in the Life Sciences (preprint)[2024]