Semi-automated colony-forming unit counting for biosafety level 3 laboratories

Summary

Obtain CFU counts using image processing with Fiji and CellProfiler, and visualize dose-response relationships across drug concentrations using R.

These companion programs are to help automate and follow along with the STAR Protocols paper.

Instructions

To run the tutorial, download three files:

1. example.zip
2. images.zip
3. results.zip

Unpack the example.zip and results.zip files alongside each other. Then unpack images.zip inside the data/ directory that was unpacked from example.zip.

This organization separates the unmodified input source data from the code and output results (Wilson 2017):

1. data/ contains the raw unedited images and spreadsheet describing the images,
2. results/ contains the output generated from the programs in code/. The numeric prefix in results/ matches that in code/ to indicate which results are generated by programs in the corresponding directory. The results/ are provided to check important intermediate calculations that are illustrated in the protocol step-by-step figures. Finally,
3. code/ generates results from the data/ and any previous results. The code is organized into subdirectories named according to the tool or the intended result.

After unzipping the three directories, the file hierarchy should appear as follows:

$ tree -F --filelimit=10 --noreport *
README.md  [error opening dir]
code/
├── 01-fiji-imagej-macros/
│   ├── ColonyMacro1.ijm
│   ├── ColonyMacro2.ijm
│   ├── ColonyMacro3.ijm
│   └── ColonyMacro4.ijm
├── 02-cellprofiler/
│   ├── ColonyCounter.cpproj
│   ├── random-forrest.model
│   └── training-set.csv
├── 03-spreadsheet-cfu/
│   └── cellprofiler.R
└── 04-plots/
    └── plot_abx_cfu.R
colony-counting.Rproj  [error opening dir]
data/
├── images/  [11 entries exceeds filelimit, not opening dir]
└── metadata.csv
results/
├── 01-fiji-images/  [78 entries exceeds filelimit, not opening dir]
├── 02-cellprofiler-analyst-spreadsheet-counts/
│   ├── ColonyCountDB.db
│   ├── ColonyCountDB.properties
│   └── random-forrest-classfied.csv
├── 02-cellprofiler-spreadsheet-counts/
│   ├── Artifacts.csv
│   ├── Colonies.csv
│   ├── ColoniesUnsplit.csv
│   ├── ColoniesWithArtifacts.csv
│   ├── ColoniesWithArtifactsUnsplit.csv
│   ├── Experiment.csv
│   └── Image.csv
├── 02-images-colonies-overlay/  [117 entries exceeds filelimit, not opening dir]
├── 03-spreadsheet-cfu/
│   └── abx-cfu.csv
└── 04-plots-cfu/
    ├── fiji-time.png
    └── log-log.png

References

[1] Wilson, G., Bryan, J., Cranston, K., Kitzes, J., Nederbragt, L., and Teal, T.K. (2017). Good enough practices in scientific computing. PLoS Comput Biol 13, e1005510. 10.1371/journal.pcbi.1005510.