Cimini Lab resources
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-October-17
Jump to:
| About us | Work with us | Software | Educational materials | Papers |
About us
Current lab preprints (from Beth’s CV)
Beth’s Broad bio page with contact email
Work with us
Learn about our collaboration models
Image Analysis Collaboration: A Practical Guide
Office hours link (free for anyone! just show up!)
CellProfiler annual support plan
Tool contributions you could make (from Google Summer of Code 2025 proposal)
Attend our semi-annual bootcamp
Software we make
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 |
 |
 |
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|---|---|---|---|---|
| CellProfiler | CellProfiler Analyst | Piximi | Distributed Something | Bilayers |
CellProfiler
Open source image analysis software. Highly flexible workflow management tool with a robust plugin system.
| Download CellProfiler | CellProfiler Manual | CellProfiler on GitHub | CellProfiler Plugins Documentation | CellProfiler Plugins on Github |
Learn to Use CellProfiler
| CellProfiler Tutorials | CellProfiler Video Tutorials | CellProfiler Examples | CellProfiler Help Forum | CellProfiler pipeline suggester |
Papers about CellProfiler
CellProfiler-plugins, 2023
CellProfiler 4, 2021
CellProfiler 3, 2018
CellProfiler Analyst
Open source data exploration software.
| Download CellProfiler Analyst | CellProfiler Analyst Manual | CellProfiler Analyst on GitHub | CellProfiler Analyst Help Forum |
Papers about CellProfiler Analyst
Piximi
Open-source, browser-based platform for interactive bioimage analysis. User-friendly interface for annotation, segmentation, classification, and quantitative measurement of microscopy images.
| Piximi.app | Piximi Manual and Tutorials | Piximi Video Tutorials | Piximi on GitHub | Piximi Help Forum |
Papers about Piximi
Distributed-Something
Run almost any encapsulated docker container in the Amazon Web Services infrastructure.
| Distributed-Someting on Github | Distributed-Something Documentation |
Distributed Tools
| Distributed-CellProfiler | Distributed-Collate | Distributed-DeepProfiler | Distributed-Fiji | Distributed-HelloWorld | Distributed-OMEZarrCreator |
Papers about Distributed-Something
Bilayers
Open-source specification designed to characterize software containers in terms of expected inputs, outputs, and tunable parameters. Its primary aim is to make bioimage analysis deep-learning algorithms more accessible by automatically generating intuitive, no-terminal-required user interfaces.
| Bilayers documentation | Bilayers on GitHub | Bilayers on Dockerhub | Slide deck describing idea of Bilayers | Bilayers video tutorial | Old demo application of Bilayers |
Educational materials
Jump to:
| Educational papers | Things we lead | Major contributors | Minor contributors |
Educational papers we wrote
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]
Things we lead
The Scientific Community Image Forum - Forum.image.sc / Paper - Scientific Community Image Forum: A discussion forum for scientific image software[2019]
Ask Erin/Dear Beth image analysis tips video podcast / Resources from podcast episodes
Bioimaging Guide - English / Spanish / Portuguese / Czech
The Image Based Profiling Handbook
The Cell Painting Gallery (image repository) - AWS RODA Website / Explore on Quilt / See featured on the National AI Ready Resource (NAIRR) Pilot website / Paper - Cell Painting Gallery: an open resource for image-based profiling[2024]
Bioimage Analysis Beginnings Broad Bootcamp (week-long paid course)
Things we are major (but far from sole) contributors to
Global Bioimage Analysts’ Society (GloBIAS) Global Registries - For bioimage analysts / For bioimage analysis trainers
Virtual I2K Meeting - 2023 edition / 2024 edition / 2025 edition
Things we contributed to (but others led)
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
Boston BioImage Analysis Society (BostonBIAS) - sign up form
Cold Spring Harbor Quantitative Imaging Course (two-week paid course)
Papers you might find useful
Full list of lab papers and preprints
Jump to:
| Profiling | Tools and methods | Reviews | Community Surveys | Opinions/Perspectives |
Profiling protocols and methods
Interpreting image-based profiles using Morpheus and single-cell visualization[2023]
Optimizing the Cell Painting assay for image-based profiling[2023]
A genome-wide atlas of human cell morphology[2024]
Live-cell painting: Image-based profiling in live cells using acridine orange[2025]
Alternate dyes for image-based profiling assays[2025]
Computational tools and methods
ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis[2020]
Reproducible image-based profiling with Pycytominer[2025]
Reviews
Open-source deep-learning software for bioimage segmentation[2021]
Defining the boundaries: challenges and advances in identifying cells in microscopy images[2024]
Community Surveys
2020 BioImage Analysis Survey: Community experiences and needs for the future[2021]
Bridging Imaging Users to Imaging Analysis - A community survey[2023]
2024 survey results - forum post / repository
Opinions/Perspectives
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 [2025]