Ask Erin / Dear Beth files

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

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 - Coming Soon!		BBBC030, BBBC031	Both CC BY 3.0	ilastik website, Tutorial for combining ilastik and CellProfiler
Episode 12 - Importing Object from Outline Images in CellProfiler- Coming Soon!	Pipeline available here	Images available here	CC-0
Episode 13 - How to Train a Pixel Classifier - Coming Soon!

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