Coverslip adapters for slide holders
Dyche designed these adapters that allow you to use a coverslip in a stage holder that accepts standard slides: https://3dprint.nih.gov/discover/3DPX-017720
Dyche designed these adapters that allow you to use a coverslip in a stage holder that accepts standard slides: https://3dprint.nih.gov/discover/3DPX-017720
Some configurations need a spacer between a Nikon microscope Ti2 base and an ASI MS2000 stage. For example, with a Bioptechs’ objective spacer, the stage must be moved up. Two models with different heights. Print 2x copies.
File here: https://3dprint.nih.gov/discover/3dpx-014906
Download this design from the NIH 3D Print Exchange: Nikon Ti2 eyepiece tube filter holder
This allows you to put a multi-band emission filter in your eyepiece tube of a Nikon Ti2 microscope to block any laser light, for laser safety when doing TIRF or other laser-based illumination. Inspired by Kurt Thorn’s version for the Nikon Ti-E scope. (More info here.)
Matlab code for tracking edge of cell and extracting kymographs. Github repository here: https://github.com/mullinslabUCSF/edge-kymograph
From:
Initiation and disassembly of filopodia tip complexes containing VASP and lamellipodin
Karen W. Cheng, R. Dyche Mullins
MBoC 2020
https://doi.org/10.1091/mbc.E20-04-0270
MEETINGS
Unless there are serious extenuating circumstances you should attend all Lab Meetings and Journal Clubs. Regular meetings and discussions are essential to building intellectual capital and a sense of community in the lab.
A. Lab meeting. This is for brainstorming and catchinb up on each other’s work. Bring your lab book and show your actual data.
B. Journal Club. If you are presenting, make certain everyone has the reference well in advance. Everyone who attends should read the paper beforehand and be prepared to discuss it critically.
C. Meeting one-on-one with an advisor
Here is a tutorial / guide on how to use ChimeraX with 5D light microscopy:https://www.rbvi.ucsf.edu/chimera/data/light-apr2017/light4d.html
It is on the ChimeraX web site under the Tutorials section, and also there is a link on the left side of the main ChimeraX web page called Presentations:https://www.rbvi.ucsf.edu/chimerax/
Here’s another tutorial about how to place markers on time series in Chimera (this can also be done in ChimeraX but user interface is slightly different) using Lil’s collagen filament time series as an example:https://www.cgl.ucsf.edu/chimera/data/markers-may2017/markers.html
Also there are details about how we handled Lil’s data in Chimera and ChimeraX
Download the design from the NIH 3D Print Exchange: box for 24x50mm coverslips
This box is for storing and transporting 24×50 mm coverslips after they have been cleaned or treated.
We wanted some coverslip spinners to dry coverslips after washing and rinsing. It’s way faster than blowing them with air. Nico kindly gave me his 3D design file for the coverslip holder, and I modified the box design from here.
Here’s a parts list (Digikey part numbers unless otherwise noted):
Power supply/AC adaptor (3V, 500mA 5V, 1A)
T975-P7P-ND 1470-2771-ND
3V DC motors (2)
P14355-ND
wired in parallel
Momentary switch
CKN1123-ND
Enclosure
377-1220-ND
Cushion feet (4)
SR52-ND
Screws for motors
Mcmaster-Carr part 90116A009
3D print coverslip holders (2)
this design was modified from one by Nico Stuurman
works for 18 or 22 mm square coverslips
IPT file
STL file
NIH 3D Print Exchange
Safety cover
laser-cut design
plexiglass
hinges
Superglue,
These are simple scripts to control the TIRF angle with the keyboard. In Micro-Manager, you load the scripts (under Tools->Shortcuts), then direct a keyboard shortcut (“Hotkey”) to run the script. The scripts add or subtract 50 and 1000 (coarse and fine), so I set each to be a different keyboard shortcut and marked those keys with tape and sharpie. After you optimize the TIRF angle, you open Tools->Device/Property Browser in uM and copy the new value then paste it into the relevant configuration.
Zip file here: NikonTiTRIFscripts