Image analysis uses computational methods to extract and analyze information from microscopy datasets. The Biological Image Analysis Group, led by Dr. Jian Wei Tay, handles both research into and education about this topic.

We have in-house pipelines to automate common tasks such as identifying cells, tracking movement and cell division, identifying organelles and structures, as well as data analysis and visualization. Working with us, instead of starting from scratch, will save you time in the long run!

Working with us

Assisting your image analysis

Through the ALMC, we offer image analysis assistance. An assistance request is a defined, short-term project. Assistance is currently provided free of charge.

Examples of how we can assist with your image analysis are:

  • Implementation of our scripts and toolboxes
  • Development of simple scripts using official MATLAB toolboxes and functions
  • Analysis using common tools, e.g., Imaris, Fiji/ImageJ
  • Routine training of pre-existing tools (Fiji/ImageJ and MATLAB)

Collaborate with us

Collaborative projects are longer-term (e.g., multi-objective and multi-year) partnerships, where we can assist your lab with code development, data analysis, experimental guidance, and more. The expectation here is that we would be listed as collaborators as co-PIs/co-Is or key personnel.

Example of collaborative projects could include:

  • Feasibility studies for new projects and grants
  • Analysis and validation of image analysis pipelines
  • Iterative experimental feedback
  • Development of new algorithms or software tools
  • Documentation of these methods in publications or presentations
  • Regular meetings with your research team
  • Grant writing and support

We understand that trying to decide between engaging our services or collaborating can be challenging and fluid. Please reach out to us so we can discuss this with you.

Getting in touch

To schedule a meeting to discuss your project:

  1. Please send an email to biof-imaging@colorado.edu with a brief description of your analysis needs (e.g., type of images, data required).
  2. You will receive an automated reply from our ticketing system. The reply will contain a link to schedule an initial meeting with Dr. Tay.
  3. During the meeting, we will discuss your needs, as well as the scope of the work.

Recognizing our work

In general, developing image analysis code involves a significant time and intellectual contribution from our group. Our policy is for our staff to be listed as co-authors in any publications, posters, and talks for any projects we work on.

For more information, check out our policy on Recognizing the core.

Image Analysis Toolboxes

Our code is freely available on GitHub.

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: