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Bioimaging FAQ

To get access or renew it if it stopped working, just email Saskia or Ian.

Please not we can only approve access to people who are trained on at least one instrument and are either based in SLS or registered as SLS visitors for other Warwick departments (including WMS). To get a visitor form, contact Saskia or Ian. Once the form has been processed, you will need to:

* Have an induction in Life Sciences (book hereLink opens in a new window)

* Complete the Moodle SLS/WMS Waste Module (find here)

* Follow the Lab forum (found here)

In ImageJ/Fiji, use Analyze > Set Scale to put the scale in the software. Then use Analyze > Tools > Scale Bar... to put a scale bar in the image. Pixel size are in the table below. Other numbers you may require (same for both machines): Cs = 2, Acceleration voltage = 200 kV.
  JEOL 2200/FEG - K2 JEOL 2100/Lab6
80000x 0.0427 nm/pix 0.138 nm/pix
60000x 0.052 nm/pix 0.184
50000x 0.0716 nm/pix 0.22
40000x 0.0907 nm/pix 0.275
30000x 0.12 0.363
25000x 0.15 0.43
20000x 0.19 0.54
15000x 0.25 0.73
12000x 0.32 0.92
10000x 0.39 1.11
8000x 0.46 1.36
6000x 0.64 1.82
5000x 0.69 2.18
4000x 0.88 2.73
3000x 1.187 3.04

For a quick and dirty way, just use a screenshot of the display.

For a publication or thesis, you'll want the full-size images. To turn them into a nice montage, load the mrcs image stack into Fiji/ImageJ. Use the Image > Stack > Delete slice to remove any empty classes, then Image > Stack > Make Montage to make a montage. Play with the settings until you're happy.

The microscope sees many more greyscales than our eyes, and all the microscope values are in the middle. This means you should adjust the contrast. Open the .tif file in ImageJ (or FIJI) and press ctrl+shift+C. This will open a new little window with a histogram. Press the "auto" button and it should automatically adjust the contrast so you can see things. Now press "apply" and save the image.

Note you should only do this for display purposes. If you are doing class averaging and/or reconstruction, please leave the images as they are - the EM software will cope.

If you are staining or freezing grids during your booked microscope session, we can provide grids. However, if you want to prepare grids in advance, you should buy your own. I recommend grids from EM Resolutions (on Opera). For negative staining, you want Formvar/Carbon grids such as FC300Cu here

Please do not remove any tweezers from MB026. You're welcome to use them in MB026 or you can buy some from Scientific Laboratory Supplies.

Our stains are hazardous so again, please do not remove them from MB026 but you're welcome to use them at any time once you have been trained. Do not use them without training and do not show others how to use them, ask Saskia or Ian for training.

If you publish a paper with data from the facility, please give us credit! Acknowledgements on papers, posters and presentations are important to us, as they help us show that we are important to people's research.

People

If the staff of the Advanced Bioimaging RTP have significantly contributed to your research, for instance in experimental design and data processing, please consider them for authorship on your publications.

Jeol 2200FS/DiSPIM/Cryo-ultramicrotome
"We acknowledge the University of Warwick Advanced Bioimaging Research Technology Platform supported by BBSRC ALERT14 award BB/M01228X/1"

Jeol 2100Plus TEM/Leica GP2 (plunge-freezer)
"We acknowledge the Midlands Regional Cryo-EM Facility, hosted at the Warwick Advanced Bioimaging Research Technology Platform, for use of the JEOL 2100Plus, supported by MRC award reference MC_PC_17136"

We focus on biological or organic samples, either at room temperature (negative stain or resin sections) or frozen in vitreous ice (cryo). This includes purified proteins, virus particles, thin slices (sections) of cells, vesicles and latex beads, but if you have something else you want to use our equipment for please ask!
You can see our equipment here.
A good introduction to cryo-EM is Getting Started in Cryo-EMLink opens in a new window by Professor Grant Jensen from Caltech. It is available for free.
We will run practical courses to train people in using our equipment
Yes, we can train you to use our microscopes independently, the training process is outlined here. If you are based at the University of Warwick, you can then book the microscopes through our booking page. If you are based elsewhere, booking the microscope will be through Warwick Shared Services