Example Pipelines and Images:
Fruit fly cells: Identifies and measures Drosophila Kc167 cells, a highly textured and clumpy cell type: Download
Human cells: Identifies and measures human HT29 cells which are fairly smooth and elliptical: Download
Human cytoplasm-nucleus translocation assay (SBS)**: Analyzes the BioImage SBS standard image set (details). Shows illumination correction and several different methods of identifying cells. It also includes CalculateStatistics for measuring assay quality: Download (77.6 Mb zipped)
Grid of Spots: Identifies patches/spots of yeast growing in a grid format (96 well plate): Download
Tissue Neighbors: Measures number of cell neighbors in tissue sample: Download
Wound Healing: Quantifies wound healing assay: Download
Speckle Counting: Identifies nuclei and speckles and counts how many speckles per nucleus: Download
Annotation: Example labeling a cell microarray with an annotated grid: Download
Classified Colonies: Identifies and measures yeast colonies growing on agar plates, and classifies by area and color: Download A tutorial for this pipeline is available: [PDF]
Tumors: Identifies tumors in mouse lungs: Download
Convert image file format: Loads DIB image files and saves them as TIF files: Download
Invert For Printing: Inverts RGB fluorescence microscopy images from a black background to a white background: Download
Worm cells: Identifies intensity of DNA content before and after division in a very simple analysis of cells - the human and fly examples are more advanced: Download
GrayToColor: Combines grayscale channel images to RGB color: Download
ColorToGray: Separates a color image into its component channels in grayscale: Download
CellProfiler Analyst Examples:
Example database and images: 1536 Human images Download (1.04G zipped)
*Note: these movies are large format .mov files and will not be fully viewable from within your browser window. It is best to right-click the download link and save them to your computer and then view them with Quicktime or VLC media player.
Exploring image data Download (5.5 mins 33MB)
Scoring cell populations Download (3 mins 23MB)
Classifying cells with machine learning Download (7 mins 38.5 MB)
How do I get started?
1. Select an example where the cell type (or object type) resembles yours. Mouse over the images for examples of CellProfiler analysis.
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| Fruit Fly example cells are highly textured and clumpy. | Human example cells are fairly smooth and elliptical. | Colonies are very uniformly round. | Grid of spots |
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| Tissue samples contain cells that are irregularly shaped with adjacent edges. | For Wound Healing assays, the cell monolayer is identified as a whole, rather than as individual cells. |
2. Download the example pipeline you chose and run it to see how it works. Adjust that pipeline to identify objects properly in your own images. This most often includes changing the rough size range of the objects. See the tuturials for step by step instructions, in the the other Papers describing CellProfiler.
3. Once you've identified cells and their compartments properly, look at example pipelines that measure phenotypes of interest and adjust your pipeline. For example:
A) The Example Fly and Example Human pipelines demonstrate general measurements like count, size, shape, intensity and texture in various compartments of cells.
B) The Human cytoplasm-nucleus translocation assay (SBS) pipeline demonstrates how to use illumination correction for more accurate intensity measures, how to calculate ratios of measures, and how to calculate assay quality measurements (Z' factor).
C) Speckle counting pipeline demonstrates how to count and measure small objects (e.g., speckles) inside larger objects (e.g., nuclei).
D) Tissue Neighbors pipeline demonstrates how to measure relationships and distances between objects.
E) Classified Colonies pipeline demonstrates how to classify and count objects on the basis of any of their measured features.
F) The Annotation pipeline displays a grid plus annotation on an image.
G) The ColorToGray pipeline demonstrates how to separate a color image into its component channels.
H) The InvertedForPrinting pipeline inverts RGB fluorescence microscopy images from a black background to a white background.
4. Still stuck? See if your question has been answered on the Forum.