Control, Readout and Commissioning of the Ultra-High Speed 1 Megapixel DSSC X-Ray Camera for the European XFEL

The goal of this thesis was to develop the software and firmware basis to control and read out the 1-Megapixel DEPFET Sensor with Signal Compression (DSSC) detector, which is being built for the European XFEL (EuXFEL). The DSSC detector proposes single photon resolution at 0.5 keV photon energy, high dynamic range of 10000 photons at a very high frame rate of 4.5 MHz. During this thesis, the readout chain has been implemented, which receives the average data rate of 134 GBit/s from the detector and transfers sorted image data via four QSFP+ fiber cables to the DAQ system. Additional control software and firmware has been developed for commissioning of the first 1/16th megapixel prototypes. A multifunctional measurement and data analysis framework has been created which is used for characterization of the detector, particularly of properties of the complex readout ASICs. Additional parameter trimming routines to automatically adapt gain and offset parameters of a large pixel matrix have been developed in order to generate suitable configurations which have been applied during two measurement campaigns at the Petra III synchrotron. For integration into the new Karabo framework, which is provided by XFEL for beamline control, several software devices have been implemented

First functionality tests of a 64 x 64 pixel DSSC sensor module connected to the complete ladder readout

The European X-ray Free Electron Laser (XFEL.EU) will provide every 0.1 s a train of 2700 spatially coherent ultrashort X-ray pulses at 4.5 MHz repetition rate. The Small Quantum Systems (SQS) instrument and the Spectroscopy and Coherent Scattering instrument (SCS) operate with soft X-rays between 0.5 keV - 6keV. The DEPFET Sensor with Signal Compression (DSSC) detector is being developed to meet the requirements set by these two XFEL.EU instruments. The DSSC imager is a 1 mega-pixel camera able to store up to 800 single-pulse images per train. The so-called ladder is the basic unit of the DSSC detector. It is the single unit out of sixteen identical-units composing the DSSC-megapixel camera, containing all representative electronic components of the full-size system and allows testing the full electronic chain. Each DSSC ladder has a focal plane sensor with 128 x 512 pixels. The read-out ASIC provides full-parallel readout of the sensor pixels. Every read-out channel contains an amplifier and an analog filter, an up-to 9 bit ADC and the digital memory. The ASIC amplifier have a double front-end to allow one to use either DEPFET sensors or Mini-SDD sensors. In the first case, the signal compression is a characteristic intrinsic of the sensor; in the second case, the compression is implemented at the first amplification stage. The goal of signal compression is to meet the requirement of single-photon detection capability and wide dynamic range. We present the first results of measurements obtained using a 64 x 64 pixel DEPFET sensor attached to the full final electronic and data-acquisition chain.Comment: Preprint proceeding for IWORID 2016, 18th International Workshop on Radiation Imaging Detectors, 3rd-7th July 2016, Barcelona, Spai

Visualization and Quantitative Analysis of Reconstituted Tight Junctions Using Localization Microscopy

Tight Junctions (TJ) regulate paracellular permeability of tissue barriers. Claudins (Cld) form the backbone of TJ-strands. Pore-forming claudins determine the permeability for ions, whereas that for solutes and macromolecules is assumed to be crucially restricted by the strand morphology (i.e., density, branching and continuity). To investigate determinants of the morphology of TJ-strands we established a novel approach using localization microscopy

First functionality tests of a 64 x 64 pixel DSSC sensor module connected to the complete ladder readout

The European X-ray Free Electron Laser (XFEL.EU) will provide every 0.1 s a train of 2700 spatially coherent ultrashort X-ray pulses at 4.5 MHz repetition rate. The Small Quantum Systems (SQS) instrument and the Spectroscopy and Coherent Scattering instrument (SCS) operate with soft X-rays between 0.5 keV - 6keV. The DEPFET Sensor with Signal Compression (DSSC) detector is being developed to meet the requirements set by these two XFEL.EU instruments. The DSSC imager is a 1 mega-pixel camera able to store up to 800 single-pulse images per train. The so-called ladder is the basic unit of the DSSC detector. It is the single unit out of sixteen identical-units composing the DSSC-megapixel camera, containing all representative electronic components of the full-size system and allows testing the full electronic chain. Each DSSC ladder has a focal plane sensor with 128 x 512 pixels. The read-out ASIC provides full-parallel readout of the sensor pixels. Every read-out channel contains an amplifier and an analog filter, an up-to 9 bit ADC and the digital memory. The ASIC amplifier have a double front-end to allow one to use either DEPFET sensors or Mini-SDD sensors. In the first case, the signal compression is a characteristic intrinsic of the sensor; in the second case, the compression is implemented at the first amplification stage. The goal of signal compression is to meet the requirement of single-photon detection capability and wide dynamic range. We present the first results of measurements obtained using a 64 x 64 pixel DEPFET sensor attached to the full final electronic and data-acquisition chain

A 64-by-64 pixel-ADC matrix

An 8-bit 5-MS/s Wilkinson-type analog-to-digital converter (ADC) cell has been designed for parallel in-pixel digitization in a 64-by-64 pixel readout ASIC. Due to its simplicity, low power consumption, and small area requirement this type of ADC is suitable for pixel-level implementations. 720-ps time stamps are generated globally by means of 8-bit Gray-code counters. They are distributed column-wise to the pixel blocks together with a conversion-start signal along 13-mm long transmission lines. The analog input voltage is sampled-and-held on a capacitor. A pixel-internal current source is used to generate a voltage ramp. The conversion into a digital word is done when the ramp voltage equals the reference voltage, and the corresponding time stamp is latched. The ASIC is fabricated in IBM's 130-nm CMOS technology. The pixel-wise gain trimming properties provide a homogeneous gain distribution. Full matrix measurements demonstrate the achievement of a signal-to-noise ratio of 70 dB when all 4096 ADCs are working simultaneously. 75 % of the pixels show DNL better than 0.4 LSB, and the INL remains within ± 0.5 LSB for 99% of the pixels. The area and power dissipation of the in-pixel ADC amounts to 100 × 120 μm2 and 150 μW at 1.2-V power supply, respectively

Tight junction networks formed by Cld3-YFP and Cld5-YFP.

<p><b>A</b>: Localization microscopy image of the region marked in the conventional wide-field fluorescence image (<b>B</b>) of YFP labeled Cld3 in HEK293 cells. More than 450,000 molecules were detected with a mean localization accuracy of ∼20 nm. The mean distance to the next neighboring molecule in the image is ∼10 nm, thus the mean effective optical resolution is only limited by the localization accuracy and yielding ∼48 nm. Magnified images of the region marked in <b>A</b> are shown in <b>D</b> and <b>E</b>. Mesh-like structures identified and analyzed by the algorithm are indicated in white. <b>C</b> represents the same region but taken from the conventional wide-field fluorescence image. <b>F</b>–<b>J</b>: Analogue visualization of Cld5-YFP expressed in HEK293 cells. Here, ∼260,000 molecules were detected with a mean localization accuracy of ∼21 nm. The mean distance to the next neighboring molecule in this image is ∼7 nm; yielding a structural resolution of ∼50 nm.</p

Densities of detected proteins and shape of the mesh-like structures.

<p><b>A</b>,<b>B</b>: Localization microscopy images of Cld3-YFP (<b>A</b>) and Cld5-YFP (<b>B</b>) with overlay of single molecule positions represented by red crosses. <b>C</b>: Histogram of the density of detected proteins on the strands of the mesh-like structures (indicated in <b>A</b>,<b>B</b> by orange arrows). Both protein types show similar distributions with mean values of ∼3700 proteins/µm². The standard deviation of the distribution for Cld3 is 760 proteins/µm². The distribution for Cld5 is wider and provides a standard deviation of 900 proteins/µm². <b>D</b>: Histogram of the density of detected proteins beside the strands of the meshes (indicated in <b>A</b>,<b>B</b> by green arrows). Here, the distribution for Cld3 and Cld5 are very similar, too (mean values: ∼780 proteins/µm² with STDs of ∼640 proteins/µm²). For many meshes (especially the very small ones) no proteins could be detected on their inside. These are not considered in the histograms. <b>E</b>: Histograms of the minimum diameter divided by its maximum perpendicular diameter of the meshes. Both protein types show similar distributions with a maximum at ratio of ∼0.7. <b>F</b>: Histograms of the extension of the meshes parallel to the orientation of the whole TJ-network (principal axis) divided by its perpendicular extension showing that the mean orientation of the meshes of both protein types is parallel to the orientation of the whole TJ-network (mean value for Cld3: ∼1.21 with STD: ∼0.38; mean value for Cld5: ∼1.29 with STD: ∼0.42). All histograms are normalized to the total amount of analyzed meshes.</p

Analysis of mesh-like structures.

<p><b>A</b>,<b>B</b>: Local point densities are visualized as grey values in the localization microscopy image. Positions of the detected single molecules are indicated by red dots. <b>C</b>: Radial intensity distribution of the mesh-like structure shown in <b>A</b>,<b>B</b>. <b>D</b>: First derivative of the radial intensity distribution. The first zero-crossing marks the position of the first maximum of the intensity distribution. A blue circle in <b>A</b>,<b>B</b> represents the approximation by the circle with a radius corresponding to the maximum of the radial intensity distribution. <b>E</b>: Histogram of the distances between the single molecule positions and the shape of the edge filter (indicated by yellow arrows in <b>A</b> for some of the positions). <b>F</b>: The first zero-crossing of the first derivative gives the distance of the majority of the points. This value is used to correct the underestimated size of the mesh obtained by the edge filter (red line in <b>A</b>). In <b>B</b> the corrected shape is illustrated by the two red lines. The area in between is used to determine the molecule density on the strand of the mesh.</p

First operation of a DSSC hybrid 2D Soft X-ray imager with 4.5 MHz frame rate

The DSSC (DEPFET Sensor with Signal Compression) collaboration develops a hybrid pixelated X-Ray photon detector with 4.5 MHz frame rate and immediate amplitude digitization for experiments at the European XFEL. We present the first full format 14.9Ã\u9714 mm2F1 pixel readout ASIC for the DSSC detector. The readout architecture is specially adapted to the burst structure of the XFEL (bursts of 2880 pulses spaced by down to 220 ns at a rate of 10 Hz) by in-pixel digitization and digital hit data storage and data transfer during the burst gaps. The readout ASIC contains 64Ã\u9764 pixels of 229Ã\u97204 μm2size and includes per pixel two low noise front-end versions for DEPFET and silicon drift detectors (SDD), a single-slope 8-bit ADC and local memory. Measurements using the F1 ASIC and a matching mini-SDD sensor matrix are shown