Hybrid Pixel Array Detector

Measurement of single crystal X-ray diffraction data

PILATUS3 R 200K Hybrid Pixel Array Detector

Rigaku Oxford Diffraction offers the PILATUS3 R 200K as the standard detector for single crystal systems. PILATUS3 R detectors are true photon counting devices that combine the following features to make them the best commercially available detectors for protein crystallography:

  • the highest sensitivity
  • the lowest readout noise
  • the fastest readout time
  • the lowest point spread function
  • fully air-cooled and maintenance free

Whether you’re collecting data for small or weakly diffracting samples or collecting data for S-SAD phasing, a Rigaku Oxford Diffraction system configured with a PILATUS3 R detector ensures the most accurate data collection for your samples. The PILATUS3 R 200K is also ideal for high throughput screening and ligand binding studies, especially when coupled with an ACTOR automatic sample changer.

Why the HPAD detector?

There are basically four types of detectors currently being used with single crystal diffractometers: HPAD, CCD, CMOS, and IP. The HPAD is the newest technology and is unique in that it is a photon counting detector that directly detects X-ray photons without the intermediate step of converting the photons to light with a phosphor.
The HPAD detector allows for shutterless data collection due to the extremely fast readout. This capability eliminates errors in the diffraction data originating from shutter timing and goniometer stop/starts, which are invariably associated with traditional data collection, and minimizes data collection time. In addition, the extremely low noise characteristics means that you can count poorly diffracting samples for a long period of time without swamping the signal with electronic noise. The combination of these features means that you will collect better data faster.

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  • Direct detection
  • Excellent point spread function – top hat
  • Excellent signal-to-noise ratio via single photon counting
  • Adjustable threshold to suppress fluorescence
  • High dynamic range: 1,048,576:1 photons per pixel
  • High counting rates: up to 2x10⁶ photons per second per pixel
  • Short readout time: 7 ms
  • Frame rate up to 20 images per second
  • Electronically gateable
  • Radiation tolerant design
  • Other PILATUS3 R format detectors are available: PILATUS3 R 300K, PILATUS3 R 1M

In addition to the PILATUS3 R 200K, Rigaku can also provide other formats of PILATUS3 R detectors, including the PILATUS3 R 300K or PILATUS3 R 1M. Specifications for each are provided below.

PILATUS3 R specifications

Number of modules PILATUS3 R 200K PILATUS3 R 300K PILATUS3 R 1M
Sensor Reverse-biased silicon diode array
Quantum efficiency at CuKα radiation > 98 %
Pixel size 172 x 172 µm²
Sensitive area 83.8 x 70.0 mm² 83.8 x 106.5 mm² 168.7 x 179.4 mm²
Format 487 x 407 = 198,209 pixels 487 x 619 = 301,453 pixels 981 x 1043 = 1,023,183 pixels
Dynamic range 20 Bits
Counting rate per pixel > 2x10⁶ X-ray/sec
Readout time 7 ms 7 ms 7 ms
Maximum frame rate 20 Hz 20 Hz 5 Hz
Point-spread function 1 pixel
Cooling Air-cooled Water chiller Water chiller
Humidity control Nitrogen or dry air flow

The PILATUS3 R detector series are designed for home laboratories to provide the best possible data collection peformance. These detectors combine two key technologies, single-photon counting and hybrid pixel technology, which eliminates detector noise and provides sharper, better resolved Bragg peaks. The following are a list of frequently asked questions regarding HPAD detectors and how they compare to other detection devices, such as CCDs and phosphor-based CMOS detectors.

How do PILATUS3 R detectors achieve direct detection?

PILATUS3 R detectors are Hybrid Pixel Array Detectors (HPADs), which convert X-ray photons directly into electron/hole pairs in the silicon wafer as shown below. Unlike other detectors they do not need to convert the X-rays into visible light as an intermediate step.


  1. X-ray photon absorbed in the Si wafer.
  2. Electron-hole pairs are generated and holes are funneled towards indium bump.
  3. Si wafter is connected to CMOS circuit by indium bumps for effective charge transfer.
  4. Pixel signal processing unit, shapes and amplifies then compares vs reference value. If above, it is counted, if below not counted.

How does a PILATUS3 R differ from a standard CMOS or CCD detector?

The primary differentiator between PILATUS3 R and both CCD (Charged Coupled Device) and standard CMOS (Complementary Metal Oxide Semiconductor) detectors is the direct detection of X-ray photons and the hybrid pixel that counts events above a threshold. Both CCD and standard CMOS detectors require the X-ray photon to first be converted to visible light as an intermediate step. Standard CMOS detectors use a fiber optic stub and CCD detectors use a fiber optic taper, and both are integrating detectors, not photon counting.


  1. X-ray photon absorbed – visible light produced and scattered in all directions.
  2. Light passes into fiber optic stub, reflection from surfaces causes more scattering and diffusion.
  3. Light passes along fiber optic stub, more scattering and diffusion before striking a photodiode.
  4. Electron-hole pairs are generated in the photodiode.
    Amplification, transmission and digitization.

Light loss, diffusion and scattering occurs at all five interfaces leading to signal loss and noise. Amplification, transmission and digitization also add noise.

But PILATUS3 R detectors contain a CMOS chip...

Correct, PILATUS3 R and standard CMOS detectors both contain devices that are manufactured using CMOS technology, but they operate in very different ways.

What are the advantages of PILATUS3 R detectors compared to standard CMOS or CCD detectors?

HPADs have some advantages over integrating detectors, such as CCDs and standard CMOS detectors. For example, both CMOS and CCD detectors convert X-ray photons to light using a fiber optic stub (CMOS) or taper (CCD). Light loss occurs at the interfaces between the phosphor-stub and stub-sensor as well as in the glass material itself. Light diffusion and light loss also occur through the fiber optic stub. As a result, CCDs and standard CMOS detectors have a point spread function with longer tails than a Gaussian causing data to spread across many pixels.

HPADs also have the advantage that they are inherently free from dark current and readout noise. The absence of these noise sources allows PILATUS3 R detectors to produce data with excellent signal-to-noise ratio.

What does ‘top-hat’ point spread function mean?

As a result of no light diffusion within the detector, PILATUS3 R spots have a ‘top-hat’ point spread function of one pixel rather than the long tail PSF seen with CMOS and CCD detectors.

Comparison of ‘top-hat’ vs Gaussian Point Spread Functions

I thought PILATUS3 R detectors were just for synchrotrons. Are they really suitable for the home lab?

Considering the main features of PILATUS3 R detectors, direct detection and single photon counting, they actually suit the home lab perfectly: recording the highest signal and lowest noise from the incident photons available.

The PILATUS3 R has a pixel size of 172 microns. Can I resolve long unit cells?

Yes, we have collected data on Mouse Angiotensinogen with resolution of the 462 Å cell axis at 260 mm. We have also resolved the 616 Å edge of a ribosomal subunit at 200 mm.

The ability to resolve reflections is attributed to the single pixel point spread function. By comparison, other detector types (CCDs, phosphor-based CMOS and IP detectors) have large point spread functions. As a result, the PILATUS3 R detector can resolve reflections as well as, or in some cases better than, other detectors. The picture below shows an example diffraction image for a thaumatin crystal collected on both a CCD and PILATUS3 R whose pixel sizes are 90 and 172 microns, respectively. Despite the larger pixel size, the PILATUS3 R is able to resolve the long axis of 150 Å by virtue of the single pixel point spread.

Thaumatin diffraction images showing well resolved reflections

Are the PILATUS3 R detectors offered by Rigaku the same detector I use at the synchrotron?

Yes, however the home lab versions (R series PILATUS detectors) run at 20 Hz or 7 ms readout time.

Can the PILATUS3 R operate in shutterless mode as I do at the synchrotron?


How do I calculate a strategy when using shutterless mode?

The data collection strategy protocol is the same for both shutterless and conventional data collection with regard to desired completeness and redundancy. In the case of shutterless data collection, you have the advantage that you can collect narrower images without the penalty of longer data collection times. This can be an invaluable benefit for samples whose orientation or mosaicity are not ideal.

What are the cooling requirements for PILATUS3 R detectors?

The PILATUS3 R 200K-A detector is fully air-cooled and maintenance-free. PILATUS3 R 300K and 1M use low-maintenance, closed-circuit water cooling for temperature stabilization at 23° C.


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