Bioimaging FAQ

We have an annual, MB26-specific induction of which we maintain a digital record using a web form. This also includes a code of conduct and a few safety questions covering the oxygen depletion system.

When you fill in the form (correctly), you will get access to MB26 until the next October, after which it will automatically lapse and you will have to fill in the form again. This ensures we have a proper record of everyone’s inductions and that all users get any important updates to the induction when they renew.

Fill in the MB26 induction form.

Please note 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 SLS inductionLink opens in a new windowLink opens in a new window)

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

* Follow the Lab forum (follow lab forum)

In ImageJ/Fiji, use Analyze > Set Scale to put the scale in the software. The pixel size from the table below goes in the Known Distance box, Distance in Pixels should be set to 1. Then use Analyze > Tools > Scale Bar... to put a scale bar in the image. Other numbers you may require (same for both machines): Cs = 2, Acceleration voltage = 200 kV.

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.

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 credit us according to the Fair Attribution Policy. Authorship and acknowledgements on papers, posters and presentations are important to us, as they show that we are important to people's research and ultimately help us get more funding.

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"

JEOL JSM-IT800 (cryo-)Scanning Electron Microscope

"We acknowledge the University of Warwick Advanced Bioimaging Research Technology Platform supported by MRC grant MR/Y002946/1"

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 windowLink opens in a new window by Professor Grant Jensen from Caltech. It is available for free.

For academic users (internal and external) costs are currently (2022) as follows:

This works out as under £500 for up to 5 samples for embedding and sectioning (including embedding, sectioning and imaging). A cryo-sample takes about an hour per sample.

DO NOT USE THESE as grant costings, please discuss any grant costings with R&IS

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

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.

To keep the samples vitrified we need to keep them below -160C. Dry ice is too hot and will not work. To ship safely using liquid nitrogen you need to use a dry shipper, which has a zeolite inside with a very high heat capacity that keeps temperature for several days even when the nitrogen has been poured out. We have a dry shipper available that can be borrowed but this needs to be agreed (and cooled down!) ahead of time. The facility you are using should have liquid nitrogen storage, so please don't leave sample prep till the last moment - if something goes wrong with the shipping you may lose your timeslot!