Difference between revisions of "User:Kevinly"

Revision as of 19:16, 17 October 2022

This Wiki page is a comprehensive compilation of Kevin's personal memos for each Assignment and component of 20.309. The intended audience is just Kevin, but if others read it and happen to learn from it, then that's nice too. Perhaps in the future, when there is a new generation of 20.309 instructors, these logs and memos will be a valuable resource.

Kevin at the Royal Observatory Greenwich in the UK to see John Harrison's clocks. The exhibits were unfortunately closed the entire week of his visit.

This page is loosely organized by Assignments/Labs.

Assignments

Assignment 1: Optics boot camp

Overview

1. Work on mystery negative lens on paper before going to the lens station
2. Verify lens-maker formula
3. Become familiar with MATLAB indexing and plotting of single/multiple pixels

Lab notes

• The lens-maker-verifying component is already built and tucked away in the cubbies in the lab

Assignment 2: Brightfield transillumination microscope

Overview

Coding notes

Lab notes

• Aligning the aluminum mirror

Assignment 3: Single-color epifluorescent microscope

Overview

Lab

Assignment 4: Resolution and particle tracking in glycerin

Overview

• Measure the resolution of their optical system (40x Nikon with 125mm tube lens and 590nm light); Expect resolution around 625nm

Lab notes

• The PSF beads for measuring the resolution are particularly small
  • Set the gain to max and use a exposure of about 200,000 µs when focusing and searching for a good patch of beads
  • When you actually take the PSF image, you can lower the gain and expect an exposure of about 800,000 µs (with current around 0.5 A)
  • Some slides are better prepared than others (the older slides are photobleached)

• Preparing the sample slide with particles diffusing in glycerin
  • Make a channel on a glass slide using two double-sided tape with a cover slip sandwiched on top. Then let the glycerin-bead mixture capillary action its way through before sealing each end of the channel with nail polish
  • You'll have to let the slide sit for a while because there may still be flow from the capillary action movement
    • Even if there is flow, you can account for it using the difference trajectory
  • Its better to do this with higher concentration of beads (10~30 in the FOV)

Assignment 5: Particle tracking in cells

This Assignment is known for applying the particle tracking code from Assignment 4.

Lab notes

• Try to find about 2-5 beads in a cell
• Helpful to have a transillumination light source on (but very dim or angled away) while the fluorescence is on (exposure around 100,000 µs)
  • This allows you to ensure the found beads are actually in treated/untreated cells

Code notes

• Bug: 3xN output of FindParticlesInMovies.m (input to Track.m) doesn't work sometimes (namely for fixed beads)
  • Error: Track.m: 'You are not going any further, check your params and data'; 'the code broke at line 1045'
  • Solution: Don't put the whole 3xN centroidWithFrames into Track.m input — just put as many frames in as possible before Track.m fails

Lab Chore Tutorials

Cleaning camera sensors

With the new camera sensor wipers that Steve ordered (they're actually designed for DSLR camera sensors), this Lab Chore is much easier (and almost fun). The traditional method was to use lens cleaning tissue, but sometimes that left lint or deposited even more dirt. The key with cleaning lenses and sensors is to firmly wipe it once.

• New cleaning method:
  1. Wet one side of the wiper with the cleaner fluid
• Old cleaning method:
• General cleaning tips:
  • Never have the exposed camera sensor angled upward; dirt and dust settles downwards!
  • Wipe once

Set screw guidelines

There are a handful of microscope parts that use set screws: C6W, CP02, and the cage rods.

Microscope Kit Assembly

The microscope parts need to be pre-assembled into a kit. The kits do not include any mirrors or filters because these parts are more fragile — hand these components to students when they finish the rest of their build.

I divide the microscope build into 3 parts:

1. Brightfield transillumination (Assignment 1)
2. Two-color epifluorescent (Assignment 3 & 8)
3. Microfluidic system (Assignment 9)

Here are the kit parts, counts, and other notes/recommendations:

Cell Culturing Protocols