Image analysis uses computational methods to extract and analyze information from microscopy datasets. We can help by developing customized pipelines to automate tasks such as identifying cells, tracking movement and cell division, identifying organelles and structures, as well as data analysis and visualization.

Our services

  • Project consultations and programming support
  • Short term projects*
  • Long term collaborations and code development*

*Note: Services are free but we ask that you consider including us in your grant for larger scale projects.

Getting in touch

We strongly encourage you to reach out to us to discuss image analysis before starting large collection runs. There are many experimental aspects that can make the analysis much easier and more robust.

To schedule a meeting to discuss your project, please send an email to with a brief description of your analysis needs (e.g. type of images, data required). We will reach out to find a suitable time, usually within 2 - 3 working days. It helps to have an example image or two for this meeting.


Developing image analysis code can involve a significant time and intellectual contribution from our staff. Please consider co-authorship if the analysis goes beyond routine analysis. For more information, check out our policy on acknowledgments.

Image Analysis Toolboxes

Most of our code is freely available in the BioFrontiers Gitlab site.

Update March 2021: BIT has informed us of an attempt to hack in to the Gitlab instance. This has forced the site to be temporarily placed behind the university firewall. If you are off-campus, you will need to use the CU Boulder VPN for access. We apologize for the inconvenience.

Training and Workshops

We are developing new workshops and material for image analysis. In the meantime, have a look at the following online training material: