• Interface: A controller PC that uses Harmony software. It also can remote-connect to a second PC that uses PlateWorks software to control both the robot and the Phenix, calling on imaging protocols saved within Harmony.
• Confocal: Spinning discs with fixed pinhole size of 50 um (or option to image in widefield mode)
• Microplates: Please note that these objectives are optimized for a plate bottom thickness of 0.17 mm but the 20x air objective has a correction collar to accommodate 0-1.5 mm thickness. The plate bottom should be glass or imaging-quality plastic, with black walls (such as the PhenoView plates from Perkin Elmer). Or we also have a holder for classic slides.

• Flex robot for sample loading to the Phenix

  • For high throughput screening (with automated imaging)
  • Samples are loaded from either a cell incubator or a room temperature plate hotel.
  • The incubator has the same racks as the incubators on our Explorer workstation, and they can be interchanged so plates can be moved in batch between the workstations.
• Other special capabilities: "Preci-Scan" for zooming in on rare events after a low mag snapshot, stitching together multiple sites from one well, flatfield correction, 3D visualization of Z stacks. See the bioinformatics page to read about segmentation, quantification, and statistics built in to Harmony.

We do not currently offer:

• additional colored lasers, higher power lasers, deconvolution, heating to temperatures other than 37 degrees, optical phase contrast, different sized pinholes, simultaneous capture of two channels using the same excitation laser.
• the following that are optional packages could be acquired with your contribution:
• the onboard pipetor. If you need to add reagents before or between measurements, we suggest you do so by manually taking your microplates to our separate dispensers, robots, or use a multichannel pipet. 
• up to two additional cameras are possible for optimal speed of simultaneous channels.
• 40x water objective

• Objectives currently available on the CSC Phenix:

*theoretical values of depth of focus, xy resolution (r), and z slice spacing is based on the numerical aperture (NA) and an average wavelength.

Working distance (WD) is the distance from the lens to the focal point (therefore it includes the width of the microplate bottom or coverslip normally excluded from WD usually published for microscope objectives).

Please note that these objectives are optimized for a plate bottom thickness of 0.17 mm but the 20x air objective has a correction collar to accommodate 0-1.5 mm thickness.

• Lasers: four excitation laser lines (405, 488, 561, and 640 nm) and one long wavelength laser for autofocusing via two peaks detection of the plate and well bottoms.
• Detectors: Two sCMOS cameras for simultaneous imaging of two channels in confocal mode. Note that the two cameras are capturing light from spatially separated illuminated regions of the sample, so there is no crosstalk/bleedthrough (unlike for a classic point scanner's simultaneous imaging). Also note that because of this, the two cameras use separate light paths and therefore are associated with specific channels:
  
  • one camera for 405 nm and 561 nm excitation
    • 435-480, 435-550, 465-480, or 465-530 nm filters for 405 nm excitation
    • 570-630, 571-596, or 605-630 nm filters for 561 nm excitation
  • one camera for 488 nm and 640 nm excitation, usually used with these emission filters:
    • 500-530, 500-550, or 515-550 nm filters for 488nm excitation
    • 650-680, 650-760, or 690-720 nm filters for 640 nm excitation
• Therefore to take advantage of the two camera system, you must image your DAPI or TRITC at the same time as your FITC or Cy5.
• Other excitation/emisssion combinations might be possible in certain cases, and almost all combinations are possible in widefield mode. The possible combinations are listed below, with possible being defined as those that are physically capable of being lined up in the filter wheel and readily selectable in the Harmony software (Y=yes, N=no). For more details, see the filter inventory.

We have Perkin Elmer Signals Image Artist bioinformatics package, Spotfire, and a second copy of Harmony software on a computer workstation in the lab space. It is currently directly networked with the Phenix imager controller PC for fast data transfer.

Computer specifications:

2 x Xeon Gold 6226R CPU w/ 16 cores each
128 GB RAM
500 GB SSD for OS
72 TB RAID5 disk array (6 x 16 TB SAS drives)
10 GbE copper NIC
Power supply:
1400W at 181VAC – 240VAC
1100W at 100VAC – 180VAC

Click here to read Perkin Elmer's flyer showing how different variables influence the speed of image acquisition. One of the figures is shown below – note that we have a 2-camera system which helps make it faster for even numbers of channels.

The samples can either be slides (we have a special slide holder for that) or microplates.

Required microplate properties:

• standard size in XY
• clear bottom (they are imaged from the bottom i.e. inverted lightpath)
• sturdy hard plastic (so the robotic stage can grip the plate well)

Strongly suggested microplate properties:

• flat bottom (the autofocus has an easier job)
• black wall (reduces fluorescence noise)
• square well (so you can capture more square sites per well)
• skirt height below 0.3mm (in z direction) if you want to use 63x objective
  • if the bottom is too close to the bench (no skirt rising it higher), it will scratch
  • if the bottom is too high off the bench (long skirt and raised wells), the objective will crash into the skirt when it tries to get near the edge wells, and so you won't be able to image the region closest to the edge, especially a problem for short working distance objectives (to get high numerical aperture, they capture light at a wider angle, so they must be close to the plate) and water immersion objectives (because they have a collar around them maintaining the bead of water on the objective).

Optional microplate properties:

• sterile for if doing cell work in them
• tissue culture treated for cell culture in them (or polylysine or collagen coated as needed)
• lidded for convenience
• barcoded if you plan to use pick lists and/or process lists on the Echo or PlateWorks

Suggested microplates – PhenoPlate brand from Perkin Elmer.

• Here is the detailed spec sheet for the 384 well format PhenoPlate. Note that if you see Cell Carrier Ultra brand plates, these are the same product renamed.