Getting Started

Software Used

In this lab we primarily use Python for controlling instruments and analyzing data. The Anaconda distribution of Python has most all of the packages we use and can be downloaded here.

We keep an organized collection of articles using Zotero which can be found here.

Other free or open-source software used:

• Fiji for image analysis

• Micro-manager to control our SPIM

• OpenSCAD for designing parts to be 3D printed

• Inkscape for making publication-quality figures

You can also find our software written in-house on our GitHub site:

• Particle tracking code and Jupyter notebook demonstration

• Differential dynamic microscopy code

Getting Acquainted with Microscopy

As we use and develop optical microscopy techniques quite a bit, you should get familiar with the theory and concepts of light microscopes. A great place to start is the microscopy course on iBiology.org. They also have a shorter version of the course.

All the lectures in those courses are good but pay close attention to these in particular:

• Fluorescent microscopy

• Resolution in microscopy

• Point-spread function

• Fourier space

Depending on the project you work on you may also want to look into

• Mobile microscopy (if you work on Fourier ptychography or the LED-matrix/eInk microscopes)

• SPIM (if you work on the light-sheet setup)

Background Reading

You'll find the listed articles on the group's Zotero collection.

For projects using/enhancing the light-sheet microscope:

• Huisken, J., Swoger, J., Bene, F. D., Wittbrodt, J. & Stelzer, E. H. K. Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy. Science 305, 1007–1009 (2004).

• Greger, K., Swoger, J. & Stelzer, E. H. K. Basic building units and properties of a fluorescence single plane illumination microscope. Review of Scientific Instruments 78, 023705 (2007).

• Pitrone, P. G. et al. OpenSPIM: an open-access light-sheet microscopy platform. Nature Methods 10, 598–599 (2013).

For projects involving DDM:

• Cerbino, R. & Trappe, V. Differential Dynamic Microscopy: Probing Wave Vector Dependent Dynamics with a Microscope. Phys. Rev. Lett. 100, 188102 (2008).

• Germain, D., Leocmach, M. & Gibaud, T. Differential dynamic microscopy to characterize Brownian motion and bacteria motility. American Journal of Physics 84, 202–210 (2016).

For projects using Fourier ptychography:

• Tian, L. & Waller, L. 3D intensity and phase imaging from light field measurements in an LED array microscope. Optica 2, 104 (2015).

• Zheng, G., Kolner, C. & Yang, C. Microscopy refocusing and dark-field imaging by using a simple LED array. Optics Letters, 36, 3987–3989 (2011).

Other Resources

• Talk on colloidal particles (Harvard colloquium)

• Talk on colloidal suspension rheology

• Talk on dynamics of biological tissue (NYU colloquium)

• Talk on advanced microscopy techniques (UC Berkeley colloquium)