Training materials and tutorials

Basic lab training material

• Shared Google document for lab “bootcamp”
• The document above has multiple parts, including:
  • Guide to maintaining a lab notebook
  • Safety and wetlab techniques
  • Microscopy usage
  • Computational / analysis methods:
    • Fiji/ImageJ
    • Python

More on microscopy

We use multiple microscopy methods in our lab. Above, there is the link to our quick tutorial on using our microscopes. We also have a short guide on using the Olympus IX73 (we have two of these microscopes in Shiley Center for Science and Technology, one in SCST 255 and one in SCST 292).

In addition to those inverted microscopes we use for wide-field imaging, we also have access to a Nikon confocal microscope in SCST 148. We also use two custom-built light sheet (or selective plane illumination) microscopes in our lab in SCST 255.

There are also a lot of very nice tutorials and guides at MicroscopyU. For instance:

• Introduction to fluorescence microscopy
• Inverted microscope optical pathway
• Useful magnification ranges
• Properties of microscope objectives
• Introduction to confocal microscopy concepts

For guides on using more specialized types of microscopy we use in the lab:

• Overview of light sheet fluorescence microscopy from MicroscopyU
• Selective Plane Illumination Microscopy (SPIM) guides from OpenSPIM
• High NA single-objective light-sheet paper

It is important to review these resources before using the microscopes in lab!

More on computational methods

As describes in the main lab bootcamp training document we use Python and ImageJ/Fiji pretty frequently.

You should start by acquiring the necessary software:

• Download and install Fiji, the “batteries-included” distribution of ImageJ
  • We use Fiji for inspecting images and doing quick analyses
• Download and install the Anaconda distribution of Python

We use differential dynamic microscopy for many projects.

• Our paper on using DDM at JoVE
• The accompanying video showing DDM usage at JoVE
• Our PyDDM software package documentation
• More on DDM

Other software

• Zotero is a great application for saving/managing references
• Inkscape is a image editing program like Photoshop or Illustrator, but free to use

Rheology

We have a DHR-3 rheometer from TA Instruments.

• Watch the DHR Quickstart e-Training Course before you start
• Guide on the TRIOS software used for controlling the DHR-3
• More to learn from the rheology webinars at TA Instruments website
  • Particularly the Rheology of Soft Biomaterials webinar

Training videos

You can find a few videos on our training YouTube channel