Bioscience Imaging Facility

Use the Facility

New Users

Welcome to the Bioscience Imaging Facility (BIF)! The Bioscience Imaging Facility is an Indiana CTSI Core that houses an array of light microscopy and whole animal imaging instruments. We are located in Hansen B032 and service all interested users, including clients not associated with Purdue University. We constantly strive to provide the highest quality of service and state-of-the-art imaging capabilities - please contact us to suggest ways that the BIF can better suit your imaging needs.

If you are unfamiliar with our imaging capabilities, please begin by visiting the Techniques page, which will acquaint you with the techniques that can be performed at this facility. Please do not hesitate to contact the facility manager (abtaylor@purdue.edu) for additional consultation on how the BIF can facilitate your project.

Once you have decided that using the BIF will be right for you, please complete the following steps:

  1. Review the Policies and Fees section of the website (below).
  2. Email abtaylor@purdue.edu to schedule an initial training session.
  3. Fill out the New User Agreement, as well as the Laser Safety Statement (for LSM microscopy) or Radiation Safety Statement (for SPECT/CT)(as necessary) and bring these completed forms with you to your training session.

After the training session, you can begin to use the facility on your own. Please schedule yourself by following the instructions in the Reservations section below. Note that PACUC-approved protocols must be acquired prior to imaging live animals. (See the Policies and Fees section for more information).

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Reservations

Please reserve BIF instruments online using Purdue's Resource Allocation Tool (RAT).

Instructions for using RAT...
  1. Select the "Bindley Bioscience Center - Imaging Facility" link.
    1. Log-in when prompted (using your ECN password)
  2. To view availablity, select an instrument and then click "View Calendar".
  3. To reserve an instrument, select "Request Reservation" in the left side bar.
    1. Select the resource and date/time that you desire. Click "Continue".
    2. Under the "Comments" section, please include any needs that may require special preparation or a specialized hardware configuration.
    3. Click "Request Reservation".

After clicking "Request Reservation", an email containing your request will be sent to the facility manager for approval. Most requests will be approved within hours, and will then appear on the calendar. In the event of scheduling conflicts that arise during the approval process, requests will be approved in the order in which they were received. At the discretion of the facility manager, experienced users may be granted the ability to reserve equipment directly.

Please cancel your reservation as soon as possible, if you will not be able to use it. At least one hour of usage time will be charged for unannounced no-shows. (back to top)

Policies & Fees

Facility Use Guidelines

  1. If you need help, ask! The facility manager is always happy to help you any time. Never reconfigure hardware yourself or tinker with the equipment. Improperly manipulating hardware greatly increases the risk of damage. Immediately report any problems to the facility manager. Unreported problems will also hinder other users and could get worse over time.
  2. All data generated at the BIF are confidential and the property of the investigator using the facility. However, the BIF reserves the right to publicly display image data in a sanitized form for advertising purposes.
  3. Equipment is reserved in the order in which reservations were received. Long-term time-lapse experiments should be run over night or on weekends to take advantage of off-hour rates.
  4. At least one hour of usage time will be charged for unannounced no-shows. Please cancel your reservation as soon as possible, if you will not be able to use it.

Animal Use Guidelines

  1. Users interested in imaging live animals must complete the "PACUC Requirements for Live Animal Imaging" form PRIOR to using the BIF. The BIF has PACUC-approved protocols ("Lumina II whole animal imaging" and "SPECT/CT whole animal imaging") that cover the process of substrate/tracer injection, the administration of isoflurane anesthesia, and the imaging process. All other aspects of experimental design related to the use of animals before, during, or after imaging must be covered by user-supplied, PACUC protocols.
  2. For animal imaging, animals must be housed at the imaging facility in Hansen. The animals must originate from either A) a commercial vendor, or B) the transgenic mouse facility. Animals ordered from a vendor should be shipped directly to Hansen. Except in very special circumstances, transport of animals from other campus locations to Hansen for housing or imaging is not permitted.
  3. The BIF provides gas anesthesia via an Univentor isoflurane vaporizer system for Lumina and SPECT/CT imaging. Although isoflurane is a safe and reliable anesthetic, the BIF is not responsible for animals that do not survive the anesthesia.

Acknowledgements

Please acknowledge " the Purdue Bioscience Imaging Facility " in any publication that includes image data collected at this facility. If facility staff make a significant contribution to experimental design, data acquisition, or data analysis, they can be personally acknowledged as well. Acknowledgement of assistance does not imply that facility staff have approved the interpretation or presentation of data as it is presented by the authors. Extensive collaborations with facility personnel that could result in an authorship-level contribution are possible. Please inquire for more information.

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Fees

InstrumentsPurdue (Hourly)*External (Hourly)*
Nikon Ti-S Wide-field $ 15.00 $ 23.00
Nikon C1+ Confocal $ 24.00 $ 37.00
Nikon A1R Confocal $ 30.00 $ 46.00
Nikon A1R Mutiphoton $ 49.00 $ 75.00
IVIS Lumina II $ 37.00 $ 57.00
MI Labs U-SPECT/CT** $ 64.00 $ 97.00

*Small, core specific, CTSI grants are also available to fund pilot experiments.

**For SPECT imaging, one hour of labor will be charged per imaging session to cover the costs of laboratory maintenance and regulatory overhead.

 

Other costs and benefits:

Free trial period: The BIF offers prospective users (or current users with substantially new projects) a free, one hour imaging session in order to assess how well our equipment can image your sample. Please schedule a time with the facility manager to take advantage of this opportunity.

Training fee: A one-time fee of $100 is charged for training on the Lumina or Nikon wide-field. Training the training fee for any other microscope or the SPECT/CT $200. (Up to two members from the same lab can participate in the same training session at no extra cost). This fee also covers unlimited help and the cost of laboratory expendables.

Animal housing fee: The BIF provides Allentown ventilated racks for housing animals on-site during SPECT/CT and Lumina imaging experiments. This service costs $1/cage/day.

Labor rate: Labor is charged at $64/hr (internal) / $99/hr (external) if facility staff are hired to perform experimental design, data acquisition, or data analysis.

Collaborations: Grant-based collaborations are invited. Please inquire.

Data Management

Data Formatting

  1. Microscopy: We highly recommend that all data is saved in Nikon's proprietary *.nd2 (or *.ics) format. This format stores all n-dimensions of data in a single file as well as the acquisition settings and other metadata. This file type can only be opened in Nikon's Elements software, the free (but limited) Nikon Elements ND2 Viewer, or in Image J using the ND2 Reader Plugin. If you prefer to process your data using other software, it can be easily exported as a TIFF or other common image formats. It is also possible to capture screen shots by pressing 'x' on the keyboard. (Note that 12-bit color images can not be opened in standard Windows software or MS Office).
  2. Lumina: Lumina 'images' (the picture displayed on the screen in the Living Image software) are saved as a directory of four, 16-bit TIFF images and two text files. Two of the images are 'internal' (you never see them on the screen) and are used for normalization. The 'photograph' image is the white light photograph seen on the screen, while the 'luminescence' image is the image of the luminescent (or fluorescent) signal. These images can be opened in any graphics software that supports 16-bit TIFFs (e.g. ImageJ, Photoshop). While in Living Image, using the 'snapshot' command creates an 8-bit PNG of the current view on the screen, which can be opened in virtually any program.
  3. SPECT/CT: After reconstruction, 3D SPECT and CT images are output as 16-bit NIfTI format files (*.nii). This file format can be opened directly in ImageJ or PMOD. From there, the data can be converted to a sequence of many of kinds of 2D image formats, including TIFF. PMOD also supports 'screenshots' or movies of the 3D visualizations, which are stored as JPGs.

Data Storage

Upon acquisition, all data is saved within the 'Data' folder on the acquisition computer's Desktop. Double-click the "Sync Data…" icon (located next to the 'Data' folder) to upload your data to the BIF FTP site. You may also bring your own portable storage device.

To access your data via the FTP site...

  1. Open My Computer and type "ftp://ftp.bbc.purdue.edu:11000" into the Address bar. (Mac users: Use Finder).
  2. Enter your username and password at the prompt.  (First time users: Email abtaylor@purdue.edu to obtain credentials).
  3. Work with the files as you please.

Data Analysis

After acquisition, most images will benefit from additional post-processing. These steps often include adjusting brightness and contrast, removing noise, and picking a color scheme that is most visible to the human eye. Each of these steps must be performed carefully, since they can alter information present in the image or make it less perceptible. The BIF supports a number of imaging processing software packages, whose capabilities are compared here. Users unfamiliar with the proper use of image processing techniques are encouraged to take advantage of our image processing service, especially for images that will be used in publications.

After an image has been processed, it can then be further analyzed using an array of automated quantification routines. For example, objects can be counted, their surface coordinates extracted, co-localization between object computed etc.

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