Ask Erin / Dear Beth files

Files related to Ask Erin/Dear Beth episodes - Now available on a YouTube near You!

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Episode List

Episode with link	Links to pipelines, models, or other files	Link to images	Images are licensed	Links to other resources
Episode 1 - Identifying Objects in Out-of-Focus Images in CellProfiler		folder here	CC-0
Episode 2 - Downloading Data from the IDR				Cyberduck, IDR, IDR download instructions - with great updates since we last filmed!
Episode 3 - QC on High Content Datasets using CellProfiler and Fiji	Segmentation Pipeline, FIJI montage script	Download instructions for an example plate of images	CC0 1.0	Current Protocols manuscript first introducing this approach
Episode 4 - Proprietary File Formats in Fiji and CellProfiler	Pipelines available here	idr0056-stojic-Incrnas/screenC, folder here	CC BY 4.0	CellProfiler Input Modules tutorial
Episode 5 - Handling Multinucleate Cells in CellProfiler	Pipelines available here	idr0056-stojic-Incrnas/screenC, folder here	CC BY 4.0	Learn more about CellProfiler's plugin system
Episode 6 - Load Data in CellProfiler	Example load_data.csv. Many more example load_data.csv available in the Cell Painting Gallery			Automatically make LoadData.csv from Perkin Elmer microscopes with pe2loaddata, More on Input modules (the alternative to LoadData)
Episode 7 - Segmenting Speckles in CellProfiler	Pipeline available here	idr0123-mota-mifish/experimentA, folder here	CC BY 4.0	CellProfiler example page, including a speckles example
Episode 8 - Using Plugins in CellProfiler				Learn more about CellProfiler's plugin system, CellProfiler-plugins repository , Read the CellProfiler Plugins Paper
Episode 9 - Measuring Percent Positive in CellProfiler	Pipelines available here	idr0139-lawson-fascin/screenB, idr0123-mota-mifish/experimentA, folder here	CC BY 4.0
Episode 10 - Images with 0's: Masks and Measuring Distances from 0's in CellProfiler	Pipeline available here	Images available here	CC-0
Episode 11 - Intro to Pixel Classification in ilastik		BBBC030, BBBC031	Both CC BY 3.0	ilastik website, Tutorial for combining ilastik and CellProfiler
Episode 12 - Importing Object from Outline Images in CellProfiler	Pipeline available here	Images available here	CC-0	Learn more about CellProfiler's plugin system
Episode 13 - How to Train a Pixel Classifier				Interactive Random Forest visualizer
Episode 14 - Illumination Correction in CellProfiler	Pipelines available here
Episode 15 - Why Do My Scientific Images Look Bad?		Example Speckles example dataset		Blog post on all-black images
Episode 16 - The Cell Painting Gallery, an Overview				CPG landing page, CPG documentation, CPG on NAIRR
Episode 17 - How to Write a Great Post on the Forum	Doc on what to do (and not do)			The Scientific Community Imaging Forum
Episode 18 - Women on the Street Interviews: Hard Hitting Questions at SBI2 2025				SBI2 website
Episode 19 - Conferences We've Attended Recently				SBI2 - The Society of Biomolecular Imaging and Informatics, ASCB - The American Society for Cell Biology, SLAS - Society for Laboratory Automation and Screening, Cytodata Society, ABRF - Association of Biomolecular Resource Facilities, Scipy - Scientific Python, OME - Open Microscopy Environment, I2K - Images to Knowledge, Globias - Global BioImage Analysts' Society, BINA - Bioimaging North America
Episode 20 - Intro to the Bioimaging Guide				The Bioimaging Guide, The companion paper
Episode 21 - Visualizing Common Deep Learning Image Augmentations	Pipeline available here
Episode 22 - Overview of CellProfiler's Input Modules				CellProfiler tutorials, Full-length CellProfiler Input Modules video, CellProfiler Input Modules written tutorial
Episode 23 - Introduction to the Cell Painting Assay				Cimini et al. Cell Painting Protocol Paper, CellProfiler pipelines for Cell Painting
Episode 24 - Thresholding in CellProfiler Part 1: Adaptive Thresholding for Uneven Illumination	Pipeline available here	Images here
Episode 25 - Interpreting Cell Painting Features: Classic Cell Profiler Features				Cimini et al. Cell Painting Protocol Paper, Cell Painting Assay wiki, CellProfiler manual, CellProfiler codebase

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TEMPLATE ROW | Episode X - TITLE - Coming Soon! | Pipelines available here / Coming soon! | LINK to host, folder here | CC BY 4.0 / SOME OTHER LICENSE | SOME_OTHER_RESOURCE |

Ask Erin/Dear Beth is partially funded by grants from both the NIH (P41 GM135019) and CZI (2023-329649) to BAC - but our funders aren't responsible for any of the cursing!

Bonus Episodes!

Want to hang out with Erin and Beth without talking science? Check out our bonus episodes where we talk about other stuff we love, like:

Bonus episodes with link	Links to any fun things
Episode 6.5 - In which we tell the story of how we know each other	N/A
Episode 13.5 - In which we talk about our love of GBBO - The Great British Bake Off	Erin's favorite Devonshire Splits recipe, Beth's favorite Smoked Salmon Soda Bread recipe
Episode 20.5 - HalfwayToI2K 2025 Crossover Event (some science, some talk about pizza) - Image Analysis Ask Us Anything - A special LIVE Ask Erin/Dear Beth event!	Check out the I2K conference website / Check out the HalfwayToI2K YouTube playlist!

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TEMPLATE ROW | Episode X.5 - TITLE - Coming Soon! | TITLE / Coming soon! |

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