Teaching

Introduction to open-source biology - keynote OR powerpoint

Useful code we’d like to share

Colony_segmentation_demo.png

calcColoniesOnPlate - matlab code for counting colonies on an agar plate. Code can be readily modified to work with colonies of various sizes and can separate connected colonies (using a watershed algorithm). Quick advice - (1) build a simple contraption to hold you phone/camera right above the plate (2) When marking a bounding box, avoid plate edges.
Files: calcColoniesOnPlate.m, Sample_plate.jpg


Designing our own platforms and tools

PixelArt at the Mitchell Lab - to keep ourselves busy while running gels

PixelArt at the Mitchell Lab - to keep ourselves busy while running gels

The Mitchell and Walhout labs are heading the new Maker-Space for the Program in Systems Biology. This space is open to the program's students, staff and collaborators and houses multiple platforms for designing and constructing hardware for our research. Using “Maker” tools as laser cutters, 3-D printers and programable micro-controllers we custom-engineer our own tools (from smart liquid perfusion systems to simple colorful pipette holders). The Maker-Space also hosts hands-on workshops for the UMass community interested in our Do-It-Yourself approach. Follow our Instagram account to get updates on our latest designs.

Contact Serkan Sayin about maker-space access.