On August 27, 2015, the Open MIC Workgroup held its second meeting, focusing on Image Analysis. Specifically, we discussed the topics of object counting and particle tracking using ImageJ/FIJI and Imaris. Due to the overwhelming interest in the topic, we switched to a larger conference room, which was a good thing as we maxed out the room capacity at ~40 attendees.
After general announcements regarding future meetings, Jen Lee from the MIC gave a short introduction on ImageJ and Imaris before jumping into live demos. Using both the Particle Analysis plugin from ImageJ and the spot and surface-rendering tools on Imaris, the group learned the basics of how to get their images ready for analysis, including the importance of high signal-to-noise ratios. After going through two simple examples, Jen dove into real-life images provided by 2 grad students and a postdoc from the Flannery, Ngai, and Kramer labs. As a group, we discussed approaches to best quantify the various images.
The final part of the meeting was lead by Peter Walentek, a postdoc from the Harland lab, who gave a beautiful demo of the process and tools he uses to track cilia flow in Xenopus.
Our next meeting will be on October 27th, when Dr. Lidza Kalifa of Semrock will give a seminar on SearchLight and optical filters. Look for an email announcement soon to reserve your spot (and get free lunch)!
Links/references from the meeting:
- Download ImageJ
- Download FIJI
- FIJI tutorials
- Imaris tutorials
- Analyzing Fluorescence Microscopy Images with ImageJ by Peter Bankhead [PDF]
- Peter’s Powerpoint presentation on object tracking (PW_fluid flow PDF); contact Peter or Jen for the R script.