Cimini Lab resources

Work with us

Office hours link

CellProfiler annual support plan

COBA signup form

Beth's Broad bio page with contact email

Software we make

CellProfiler

plugins documentation

pipeline suggester

papers - CellProfiler-plugins [2023] / CellProfiler 4 [2021] / CellProfiler 3 [2018]

CellProfiler Analyst

papers - CellProfiler Analyst 3 [2021]

Piximi

Distributed-Something

Bilayers

Educational materials

Educational papers we wrote

The Twenty Questions of Bioimage Object Analysis[2023]

A biologist’s guide to planning and performing quantitative bioimaging experiments[2023]

Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions[2024]

A postdoctoral training program in bioimage analysis[2024]

Stuff we make

Lab paper pages

Current lab preprints (from Beth's CV)

Imaging Platform Blog

YouTube tutorials

Office hours link

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]

Stuff 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

Papers you might find useful

Protocols

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]

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]

Opinions/Perspectives

Moving beyond the desktop: Prospects for Practical Bioimage Analysis via the Web[2023]

A Call for FAIR and Open-Access Training Materials to advance Bioimage Analysis[2024]

The Crucial Role of BioImage Analysts in Scientific Research and Publication[2024]

Building momentum through networks: Bioimaging across the Americas[2024]

Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data[2024]

Enabling Global Image Data Sharing in the Life Sciences[2024]