| Episode 1 - Identifying Objects in Out-of-Focus Images in CellProfiler |
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folder here |
CC-0 |
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| Episode 2 - Downloading Data from the IDR |
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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 |
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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 |
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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 |
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| Episode 10 - Images with 0's: Masks and Measuring Distances from 0's in CellProfiler |
Pipeline available here |
Images available here |
CC-0 |
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| Episode 11 - Intro to Pixel Classification in ilastik |
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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 |
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Interactive Random Forest visualizer |
| Episode 14 - Illumination Correction in CellProfiler |
Pipelines available here |
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| Episode 15 - Why Do My Scientific Images Look Bad? |
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Example Speckles example dataset |
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Blog post on all-black images |
| Episode 16 - The Cell Painting Gallery, an Overview |
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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) |
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The Scientific Community Imaging Forum |
| Episode 18 - Women on the Street Interviews: Hard Hitting Questions at SBI2 2025 |
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SBI2 website |
| Episode 19 - Conferences We've Attended Recently |
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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 |
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The Bioimaging Guide, The companion paper |
| Episode 21 - Visualizing Common Deep Learning Image Augmentations |
Pipeline available here |
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| Episode 22 - Overview of CellProfiler's Input Modules |
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CellProfiler tutorials, Full-length CellProfiler Input Modules video, CellProfiler Input Modules written tutorial |
| Episode 23 - Introduction to the Cell Painting Assay |
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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 |
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| Episode 25 - Interpreting Cell Painting Features: Classic Cell Profiler Features |
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Cimini et al. Cell Painting Protocol Paper, Cell Painting Assay wiki, CellProfiler manual, CellProfiler codebase |
| Episode 26 - Thresholding in CellProfiler Part 2: Picking the Right Algorithm |
Pipeline available here |
Cell Painting images from the Broad Bioimage Benchmark Collection BBBC022, download from CellProfiler's Advanced Segmentation tutorial here ;Speckle images from idr0123-mota-mifish/experimentA, folder here |
BBBC022 is CC-0; Speckles are CC BY 4.0 |
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| Episode 27 - Interpretable Deep Learning Features in Cell Painting: Anomaly Profiles |
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Shpigler et al. Paper, Cell Painting Gallery |
| Episode 28 - Thresholding in CellProfiler Part 3: Threshold Correction Factor and Limits |
Pipeline available here |
Cell Painting images from the Broad Bioimage Benchmark Collection BBBC022, download from CellProfiler's Advanced Segmentation tutorial here |
CC-0 |
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| Episode 29 - Intro to Pooled Cell Painting |
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PERISCOPE paper |
| Episode 30 - Modifying the Cell Painting Assay |
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Paper here |
| Episode 31 - Filtering Objects that Touch the Cell Edge in CellProfiler |
Pipeline available here |
Image download instructions here |
CC0 |
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| Episode 33 - Guide to Cell Painting for Biologists |
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Guide to Cell Painting for Biologists |
| Episode 34 - Interpreting CellProfiler's Image Quality Features |
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CellProfiler manual, CellProfiler Quality Control Tutorial, Bray et al., 2012 |
| Episode 35 - Working with Collaborators Part 1/3 |
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| Episode 36 - Cell Painting Feature Transformations |
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Caicedo et al. 2017, Rohban et al. 2019, Hayir et al. 2026, Arevalo et al. 2024 |
| Episode 37 - Working with Collaborators Part 2/3 - Tools |
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