The ScanCo µCT 100 is a high-resolution computed-tomography scanner for non-living samples. The scanner is capable of resolutions down to 3.5 µm. The instrument can hold up to 12 sample holders at a time to perform batch scanning. The facility has two of each of the cylindrical sample holders with the following internal diameters (in mm): 8, 12, 17, 32, 46, 71, 84, 99. 

The PerkinElmer IVIS Lumina LT is a live animal topographic imager capable of imaging most small rodents, or small objects. This system performs best when imaging luminescent transgenic rodents, but is also capable of fluorescent imaging. For fluorescence, the IVIS has ten 30 nm bandwidth excitation filters covering the full spectrum from 415 nm to 760 nm, and four emission filters:

• GFP (545/60)
• DsRed (612/75)
• Cy5.5 (732/75)
• ICG (842/65)

Any prospective user of the IVIS instrument must be listed as personnel on an approved IACUC protocol. This IACUC protocol must also contain the standard procedure for the IVIS imager. This information will be verified by the facility director prior to IVIS use.

The Azure Cielo 6 is a six channel qPCR instrument. This instrument is only compatible with semi-skirted or no-skirt low-profile 96 well PCR plates. Full-skirted or high-profile plates will not fit. Tutorial videos on the instrument operation can be found here (link). A link to download the required software for analysis can be requested from the facility director.

Copy and paste the grant write-up below for use in grant applications.

The Optical Imaging and Analysis Facility is centrally located on UB’s South Campus within the Health Sciences Complex and houses several high-end research instruments available to all university investigators and outside researchers. The instrumentation includes two fully motorized research microscopes: an Andor Dragonfly spinning-disk confocal microscope with incubation, and a Zeiss Axio Observer inverted fluorescent microscope; as well as a ScanCo µCT 100, a BD LSR SORP Fortessa eleven-color cell analyzer, a BD FACSAria seven-color cell sorter, a PerkinElmer IVIS Lumina III,  an RS 2000 small animal irradiator, a Thermo-Fisher NanoDrop One spectrophotometer, a gel imager (Bio-Rad GelDoc EZ), a multimode gel and blot imager (Bio-Rad ChemiDoc), a real-time qPCR thermocyclers (Bio-Rad CFX Connect), and a luminescence and fluorescence microplate reader (BioTek Synergy HT). The facility staff carry out an educational outreach program on best practices in data acquisition and analysis, and provide one-on-one hands-on training for all facility instrumentation. Additionally the staff are available to assist with any post-acquisition data processing and analysis needs. 

To import mgHA/ccm calibrated DICOM files from the ScanCo100 microCT into Fiji, you will need to do the following:

1. Installation:
   1. Download Fiji and extract it to a location where you have write privileges, such as your documents folder.
   2. Open Fiji and go to Help > Update... Then click "Manage Update Sites" and "Add Unlisted Site". For the new update site, put in: 
      1. Name:  ScanCo100 Import
      2. URL: https://sites.imagej.net/UBoiaf-microct/ 
   3. Make sure your new update site is set as "Active" (the checkbox is checked), then click "Apply and Close" and "Apply Changes". Restart Fiji.
2. Data Import:
   1. Make sure that the DICOM sequence you want to open is in a folder containing only those *.dcm files.
   2. Open Fiji and go to Plugins > MicroCT > ScanCo 100 import - Calibrated Data. Navigate to the folder containing your DICOM files, select the first file only, and click "Open". The plugin will use pattern recognition to open the entire sequence. 
   3. Once the image is open, intensity measurements will be reported in calibrated units. The calibration equation can be viewed by going to Analyze > Calibrate, checking the "Show plot" box, and clicking "OK." 
   4. For further discussion on utilizing calibrated data within Fiji, please schedule a consultation with facility staff.