Imaging Cores - Optical

RRID:SCR_023355

Imaging Cores - Optical receives 2021 EEF funds from RII to upgrade computer workstations

Date of publication

In May and June of 2021 the computer workstations in the RII Imaging Cores - Optical were upgraded to new HP hardware and are now running Microsoft Windows 10. The computers for the two Zeiss LSM880 instruments in Marley also received new real-time controllers, essentially a computer on a board that controls all the microscope hardware. The Zeiss Elyra S.1 received both a new instrument and post-processing computer. Other computers in Marley (LSM880 offline workstation, Stereo microscope computer) were given operating system software updates to bring them up to Windows 10.

The leftover computers have been put to good use. The image analysis workstation in LSN received a long overdue update, and the Imaging Cores - Electron facility will use one of the workstations to begin offering image analysis services. An additional Zeiss ZEN installation has been set up in the Marley location.

Our thanks to Drs Zarnescu and Eggers for submitting the LSN upgrade proposal. We also appreciate Dr. Helena Morrison for submitting the upgrade proposal for the Marley location.

The RII Equipment Enhancement Fund is designed to add or augment research capacity through the acquisition of equipment for use by multiple investigators in shared facilities or approved university core facilities.

Related Facility

RII Core Facilities - Imaging Cores - Optical - Scheduling & cancellation policy

Effective date: June 1, 2021 (revised January 21, 2025)
Applies to: RII Imaging Cores - Optical
Brief Description: Failure to cancel a scheduled reservation more than 24hrs before the reservation begins will lead to the customer being charged for the reserved time. If the available time happens to be used by a different customer, the original customer is only liable for the remainder. See policy PDF below for specifics.

Policy

TPI 1000 vibratome

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.

Image
TPI 1000 plus
Equipment
Location

Post-processing workstations

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.

Service

Image analysis

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.

Service