Frequently Asked Questions

GENERAL QUESTIONS

Is the nano CT machine (Xradia) available to everyone?

YES. The Xradia is open to everyone in academia (both internal and external to McGill University) as well as corporate industry clients. Clients, however, are not permitted to use the machine on their own. An experienced technician hired by the organization is the only individual permitted to operate the nano CT machine, but clients are welcome to come see the machine in use during the free trial scan with their prepared sample to ensure the clients are pleased with the resulting data.

How can I gain access to the nano CT machine?

All access to the nano CT machine begins with the completion of the Xradia Consultation Form. Any e-mail inquiry about the machine will be sent a link to fill out the consultation form because the required fields in the form provide a baseline amount of information for the technician to determine if the nano CT machine is appropriate for the client's intentions.

24 hours after filling out the consultation form the client will be contacted for a formal consultation to discuss the project. Details such as sample preparation, desired resolution, contrast methods, scanning charges, and the machine booking system are all discussed at the first meeting so the client fully comprehends the procedure.

Can I image my samples myself?

NO. The nano CT machine may only be operated by the technician employed by the organization. However, clients are welcome to observe the machine in use during the trial scan appointment.

How do I book the nano CT machine?

We will create an account (="study") on our online booking system for your lab/institution. The booking system will send an automated email to your supervisor informing him/her about the creation of the account (="study") and asking for his/her approval. Approval requires the PI to log into our booking system and to actively approve the account (="study"). The automated email to your supervisor will contain the link to the booking system and instructions on how to log in and how to approve a study.  Reservations for the nano CT on your behalf can only be made AFTER approval of the lab account ("study") by your PI and will be made by the technician only.

How can I access my data?

Data from the nano CT machine can be accessed one of two ways:

1. Bring an external hard drive that the technician can transfer files onto
2. The data will be uploaded to the McGill OneDrive cloud storage

Are my data safely stored on the xRadia or any IQBI workstation?

NO!
1. Bring an external hard drive that the technician can transfer files onto, or the data will be uploaded to the McGill OneDrive cloud storage
2. We do not take any responsibility for the storage of your data

What software do you recommend to analyze the 3D data?

Dragonfly (Object Research Systems; http://www.theobjects.com/dragonfly/) is recommended by Zeiss for the analysis and visualization. Alternatively, there are open source 3D visualization softwares available.

YES. You can use one of our workstations that run Dragonfly, the current price is $7/hr for academia. Access to the workstation also requires the creation of a lab/institution account (="study") on our online booking system. The account will need approval from your supervisor before booking is possible. Different than for the booking of the nano CT, you will be able to book the workstation yourself.

Do you provide analysis and/or 3D visualization of the scanned data?

YES. Full service data analysis and visualization is available upon request. The fees for this service can be found on the Fee Structure page.

TECHNICAL QUESTIONS

Are there different types of imaging techniques available?

YES. The Xradia offers several different features to accommodate a variety of samples.

- Absorption Imaging
- Phase Contrast Imaging 
- Scout & Zoom Scanning
- Stitching
- Dual Energy Imaging

What is the maximum resolution I can achieve with my samples?

In general, the resolution of the image depends on the imaging technique that is implemented. The minimum voxel size (ie. the max resolution in 3D)  that the Xradia can achieve is 700 nm. Spatially, the resolution ranges from 0.4-0.5 um to 40-50 um.

What is the maximum sample size that can be scanned?

The maximum sample size the nano CT machine is 30 x 30 x 30 cm in size and 15 kg in weight.

What is the size of the field of view (FOV) or the volume that is scanned?

                  

How long is a typical scan for a sample?

The scanning time depends on the material, contrast, and scanning parameters (ie. resolution, projections, etc.). Submicron scans, for example, typically continue overnight requiring 12-24 hours to run to completion. 

Does my biological sample need a contrast agent (ie. dye)?

If the client wishes to implement phase contrast imaging, no dye is required because phase contrast enhances the edges of materials like soft tissue. Please note that it is best to use smaller sample sizes for phase contrast imaging to be effective.

A dye is required if the client wishes to use staining for absorption imaging. Dyes can be very helpful when attempting to resolve specific features; there are several contrast agents available such as iodine based contrast agents (I2KI, I2E), phosphotungstic acid, and phosphomolybdic acid if the client wishes to discuss that option.

How do I prepare my sample for scanning?

Solid samples:
The sample must be sample during the scanning in order to provide clear images, meaning the sample should be securely attached to the sample holder. Most samples are mounted directly onto the sample holder which is taken care of by the technician. If this is not an option due to the nature of the client's sample, an alternative method can be discussed beforehand.

Wet samples:
These samples are inserted into a small plastic tube or conical tube to avoid desiccation. The plastic is optimal for imaging in the nano CT machine due to its reduced x-ray absorption properties. The tube is often stabilized using Kimwipes or parafilm.

What file format is the data characterized by?

There are four file formats available for 2D section data: .txm, .bin, .tiff, and .dicom. The data is automatically uploaded or transferred as TIFF files unless specifically requested otherwise.