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 in files or exported to a database (if large).

CellProfiler Analyst allows researchers to explore and analyze data. 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 Python, using Scipy and Numpy to implement most of its algorithms. Concerned about speed? You can also wrap C or Java code in Python, or use the Cython extension.

Check out our Developer Wiki for more information.

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. For more information about CellProfiler development, check out our Developer Wiki.

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 or CellProfiler Analyst. CellProfiler Analyst can read data from CSV files or MySQL databases; the latter might require some assistance from your IT department to set up, but it's optional.

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

You can also use Microsoft Access if you have fewer than 65,536 rows per table (but each object in your analysis is a row), 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 only a few images, should I use CellProfiler?

Using CellProfiler lets you extract quantitative information from your images, even if you only have a small number of them. However, CellProfiler is designed to run on large image sets; there is more of a payoff for large sets because the setup time for an analysis is roughly the same whether you have 5 images or 500,000.

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.

Can I collaborate with you on a project?

Like most academic research groups, we must be very selective about choosing research projects. We collaborate with academic and commercial laboratories to solve challenging image analysis problems, especially in high content screening, and in some cases we can provide help for an hourly fee. Learn more and contact us via the Imaging Platform website to explore a collaboration.

How can I show my enthusiasm for the CellProfiler project and simultaneously help a good cause?

Go here: The CellProfiler Shop

What if I have more questions?

We suggest you visit the CellProfiler forum.