Frequently Asked Questions

Are CellProfiler and CellProfiler Analyst free?

Yes. They are free and open-source (GPL). See the license.

What is the difference between CellProfiler and CellProfiler Analyst?

CellProfiler processes images and produces numerical data, which can exported to Excel (if small) or deposited to a database (if large).

CellProfiler Analyst allows researchers to explore and analyze data in a database. The machine learning-based scoring of complex phenotypes is one example of the analysis tools in CellProfiler Analyst.

Do CellProfiler and CellProfiler Analyst have to be used together?

No – while the two software packages work well together, they can be used individually:

I’m an image processing expert. Why should I use CellProfiler for development?

You can take advantage of the existing base of modules for the mundane parts of image processing and focus on developing your own algorithms or complex sequences of modules. When you have developed a solution, you can contribute the code to the open-source CellProfiler project, which saves you from writing your own GUI, compiling for multiple platformsd, and answering basic questions from the public (like installation troubleshooting and basic usage). Your method will be widely available and in a format that biologists can actually use.

CellProfiler is written in Matlab, which is commonly used in image processing, especially for prototyping. Note that many CellProfiler modules are simple wrappers for Matlab functions – the identification and illumination correction modules are where some of the more interesting algorithms reside. Concerned about speed? Matlab allows functions to be written in other languages, compiled, and called from the program.

Within CellProfiler, check out Help > General Help > DeveloperInfo for further information for developers.

I'm an image processing expert. Can I use CellProfiler modules as part of a larger software package?

Sure! As long as you comply with the open-source license, you can use pieces of the source code in your own software. You might particularly be interested in the subfunctions (CPsubfunctions folder), or in following the instructions to run CellProfiler modules “headless” (that is, without the GUI). Within CellProfiler, check out Help > General Help > DeveloperInfo for further information for developers - especially the section “Running CellProfiler without the graphical user interface”.

What happened to the CellVisualizer software project?

It was renamed CellProfiler Analyst.

I'm not a programmer. How much programming do I need to know?

No programming experience is required to use either CellProfiler and CellProfiler Analyst. Setting up databases for data in order to use CellProfiler Analyst might require the help of your local information technology group or database administrator, especially during your initial configuration of the database and software. You can learn more about MySQL databases and commands here: http://dev.mysql.com/doc/refman/5.0/en.

I don't have MySQL or Oracle, can I use Microsoft Access?

We recommend MySQL or Oracle for large datasets and any dataset where you would like to use CellProfiler Analyst. You can use Microsoft Access if you have fewer than 65,536 rows per table, by exporting the data as a CSV file using CellProfiler's ExportToExcel module or data tool. Then, you can create various tables in Access, and use another program (such as Excel) to analyze your data.

I have a small image set (20 images), should I use CellProfiler Analyst?

For simple analyses of small image sets (creating plots or sorting data by one particular measurement), it's probably more convenient to use the built-in CellProfiler data tools or a spreadsheet program like Excel after exporting your data with CellProfiler's ExportToExcel module or data tool. CellProfiler Analyst is more useful for large data sets or sophisticated analyses; it has several built in features that will help you create histograms, scatterplots, classify your data by a particular phenotype, and score your classified results. CellProfiler Analyst is a great tool for data exploration, especially if you need a simple-to-use program to help you view your data in several formats.