The TPI 1000 is available at the Marley location. A vibratome is useful for sectioning fresh or fixed tissues into thicker slices, such as 100-200um in thickness. It features an adjustable sectioning window, a bath drain, stroke pause switch, and an anti-corrosion surface. It has a total vertical specimen stroke of 15mm.

Users will need to receive training before they can access the vibratome, as the vibrating razor blade has the potential to be very hazardous.

Post-processing of image data includes:

• Exporting from propriety formats (e.g., Zeiss CZI or Leica LIF) to TIF images
• stitching of tile scans (montage creation)
• spectral un-mixing of data collected using the Quasar detector on either of the Zeiss LSM880 microscopes
• Airyscan post processing (Zeiss LSM800 confocal/multiphoton - due to software licensing issues, this is only available on the microscope computer)
• SIM post-processing and channel alignment (Zeiss Elyra S.1)
• Deconvolution of Apotome data (Zeiss Axio Observer 7 with Apotome III Microscope)

If users need these post-processing techniques, they are typically covered in the user's training on the specific instrument. The workstations are available for scheduling on iLab to approved users. If you need training or assistance, please feel free to contact us.

• Image Analysis computer workstation (LSN)
• Zeiss SIM post-processing computer workstation (LSN)
• Zeiss LSM880 post-processing computer workstation (Marley)

We have powerful workstations available with selected software programs (commercial or open source) for the post-processing and image analysis of microscope images. The workstations are available for scheduling in iLab. If you have specific post-processing needs regarding microscope data collected on our instruments, we will usually address these as part of the training on the instrument used to gather the data. Please feel free to ask us for assistance.

Depending on your needs (and our current expertise), we may be able to assist you in building an image analysis workflow. We have experience in thresholding and segmentation type analysis, but more elaborate workflows may be beyond our skillset or the capabilities of the software that we have available. Features that can often be quantitated include object counting, geometrical properties (length, area, perimeter, shape factors), and volumes can be estimated using stereological techniques. If we build a workflow, there may be a labor charge for our time. 

Our thoughts on fluorescence quantitation - the software to quantitate fluorescence intensities is easy to find. Unfortunately microscopes are known to be subject to a number of physics, engineering, and optical variabilities that are difficult to control. This means that to correctly capture fluorescence data that can be accurately quantified, the user must be willing to be meticulous in their sample prep and to ensure that the instrument variables are carefully controlled for (as a start, see The 39 Steps: A Cautionary Tale of Quantitative 3-D Fluorescence Microscopy). Controlling the instrument to ensure accurate data is time consuming and non-trivial. It is our opinion that much of what passes as quantitative fluorescence in the published scientific literature is worthless.

There are times when users need quality microscope data immediately, or they may only need a few example images to compliment other scientific data for a publication or a grant submission. Our experienced core managers are available to operate the microscopes on your behalf. The charges for assisted use are calculated at the routine hourly usage rate plus an hourly staff labor charge (rates are available in iLab).

Sample preparation strongly affects the quality of the images that can be captured with a microscope. If a user brings us a poorly prepared sample, we will give the user the best images that are possible with that otherwise compromised sample. Please consult with us ahead of time to ensure a good outcome.

While we are very familiar with our instruments, occasionally we are asked to perform an imaging method that we have not done before. This may require additional research on our part, and perhaps additional training from the vendor before we can successfully perform the new method. Depending on the amount of time involved, we may need to discuss an additional staff labor fee.

NOTE: BSL2 samples must be discussed with the on-site core manager BEFORE they arrive in the facility.

Each instrument in our core facility requires specific training by one of our core managers before a user can be allowed to operate it by themselves. The exact length of training varies due to the complexity of the instrument and the previous experience of the new user. Training is charged at the the instrument's routine hourly rate plus a per hour staff labor fee (training rates for all of our instruments can be found in iLab). The core manager makes the determination as to when the user is ready to operate an instrument by themselves.

Training is often 2-3 sessions of 1.5 hours each. Because our rooms are small, we limit the number of trainees to a maximum of two individuals from the same lab. The first session is typically instructional, with the manager explaining principles of the optics, electronics, software, and data handling. The core sometimes uses a teaching sample for the first session. The remaining sessions are hands-on with the user's sample and the user learning to operate the microscope. We teach the trainee how to get the most of the instrument and often make suggestions about sample prep, alternate techniques, controls, etc.

For many of our instruments we have written resources (available online as PDFs) and we are working on developing D2L-based training to replace the instructional sessions for most of our instruments.

Please contact us if you have any questions.

Getting the most out of our microscopes requires careful experimental design and sample preparation. We are available to discuss your research needs, review your plans, suggest changes that could improve your images, and steer you towards an instrument that is best suited to your needs (even if it is in another core). Please contact us to talk about your research needs.

Some of our microscopes can be used for BSL2 research. DO NOT SHOW UP WITH A BSL2 SAMPLE WITHOUT FIRST CLEARING IT WITH THE ON-SITE CORE MANAGER!

If your questions require us to do additional in-depth research, we are happy to do that. There may need to be a labor charge for this extra work, but that can be discussed up front.