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Summary of Contents for Dectris ARINA
- Page 1 User Manual ® DECTRIS ARINA DECTRIS Ltd. 5405 Baden-Daettwil Switzerland www.dectris.com...
- Page 2 Document Version v1.8.1 © Copyright 2024 DECTRIS Ltd.
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Page 3: Table Of Contents
EXTE - Externally Enabled Exposure Series ....... . 22 ® DECTRIS ARINA User Manual v1.8.1... - Page 4 Upload pixel-wise correction factors ....... . 27 ® DECTRIS ARINA User Manual v1.8.1...
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Page 5: General Information
1.2.2. Symbols on the Detector Attention Before operating the detector, please consult the user documentation. Danger Touching the cover foil or sensors can cause an electrical shock. Disconnect power before ser- vicing the detector! ® DECTRIS ARINA User Manual v1.8.1 1 | 29... -
Page 6: Warranty Information
(in particular information, ® images or materials), unless otherwise indicated. Without the written permission of DECTRIS it is prohibited to integrate the protected contents in this publication into other programs or other websites or to use them by any other means. -
Page 7: Safety Instructions
• Opening the detector or the power supply housing without explicit instructions from ® DECTRIS will void the warranty. • Do not install additional software or change the operating system. • Do not touch the sensor or contaminate any vacuum related part. ® DECTRIS ARINA User Manual v1.8.1 3 | 29... -
Page 8: System Description
• Short readout time and high frame rates • Shutterless operation The ARINA hybrid pixel detector is composed of a sensor, a two-dimensional array of pn-diodes processed in a high-resistivity semiconductor, connected to an array of readout channels designed in advanced CMOS technology. -
Page 9: Continuous Readout
3.2.2. Continuous Readout One of the hallmark features of ARINA is its continuous readout that enables high frame rates at high duty cycles. Every pixel of an ARINA ASIC features two digital counters. After acquisition of a frame, the pixels switch from counting in one digital counter to the other. -
Page 10: Binning And In-Pixel Compression
3.2.5. Binning and in-pixel Compression ARINA offers 2x2 pixel binning that combines 4 physical pixels into one image pixel. This is illustrated in fig- ure 3.2. With 2x2 pixel binning enabled the achievable frame rate increases by a factor of 4. As the full detector is read out in 2x2 binning mode, the field-of-view does not change when switching between different binning modes. - Page 11 The ARINA detector writes 4D scanning transmission electron microscopy (STEM) datasets in the HDF5 file ® ® format. DECTRIS provides NOVENA , a software which is able to handle 4D STEM HDF5 datasets, with the ® primary aim to display and analyze them. For more information about NOVENA please have a look at the ®...
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Page 12: Quick Start Guide
4.1. Accessing the Detector Control Unit The ARINA detector is controlled via the network interface of the detector control unit. Hence, the IP network address of the detector control unit has to be known to be able to connect to the API. Depending on the network structure, there are several ways of determining the IP network address, which are described below. -
Page 13: Using A Fixed Ip
Table 4.1: Network Settings Laptop IP Adress 169.254.254.100 Subnet Mask 255.255.0.0 Default Gateway not required With those settings, the detector can be easily configured through the web interface at http://169.254.254.1. ® DECTRIS ARINA User Manual v1.8.1 9 | 29... -
Page 14: Getting Started
• Turn on the detector control unit. Please allow at least 5 minutes for the BIOS test procedures and startup of software to complete. • Turn on the user computer. • Power on the scan generator. ® DECTRIS ARINA User Manual v1.8.1 10 | 29... -
Page 15: Web Interface Overview
6. WEB INTERFACE 6.1. Overview The ARINA web interface (figure 6.1) provides simple access to basic functions and settings of the detector system for installation, debugging, and system updates. For productive operation of the detector, please refer to the API Reference. -
Page 16: System Settings And Administration
6.2. System Settings and Administration To access the ARINA system settings, click on the corresponding tab on the homepage. The system tab allows to configure the detector control unit network settings and get some status and system information. Table 6.2 summarises menu items available for configuration Figure 6.2: Screenshot of the system settings showing the network configuration page. -
Page 17: General Usage Of The Detector System
7.1. Detector Control and Output The ARINA detector system is controlled through the SIMPLON API, an interface to the detector that is based on the http protocol and implemented on the detector control unit. The API Reference supplied with the system describes this interface in detail and allows for easy integration of the detector control into the user instru- mentation independent of the operating system or programming language being used. -
Page 18: Control Of The Detector From A Specific Environment
In external enable modes the parameter nimages is ignored (i.e. always 1) and the number of frames therefore has to be configured using the detector configuration pa- rameter ntrigger. ® DECTRIS ARINA User Manual v1.8.1 14 | 29... -
Page 19: Additional Configuration Parameters
• detector | config | flatfield_correction_applied • detector | config | pixel_mask_applied ARINA offers 2x2 pixel binning and in-pixel compression to provide high framerates. A description of these features and the achievable performance is given in section 3.2.5. These features can be controlled via the following SIMPLON API keys: •... -
Page 20: Interdependency Of Configuration Parameters
API. Below, several example CURL command prompts are provided to illustrate how to read and write detector settings, as well as interface files stored on the DCU. The examples assume the IP address of the DCU to be 169.254.254.1. Commands can be transmitted using a PUT request. ® DECTRIS ARINA User Manual v1.8.1 16 | 29... - Page 21 # Request a list of all filewriter files on the DCU curl −X GET http://169.254.254/filewriter/api/1.8.0/status/files # Download 'example_file_master.h5' file from DCU curl −X GET http://169.254.254.1/data/example_file_master.h5 −−output example_file_master.h5 # Delete filewriter file 'example_file_master.h5' on DCU curl −X DELETE http://169.254.254.1/data/example_file_master.h5 ® DECTRIS ARINA User Manual v1.8.1 17 | 29...
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Page 22: Python 3
# Arm the detector, trigger the acquisition and disam the detector client.sendDetectorCommand('arm') client.sendDetectorCommand('trigger') client.sendDetectorCommand('disarm') # Download the files from the DCU to the current folder client.fileWriterSave('example_file_master.h5', '.') client.fileWriterSave('example_file_data_000001.h5', '.') # Delete files on DCU client.fileWriterFiles('example_file_master.h5', 'DELETE') client.fileWriterFiles('example_file_data_000001.h5', 'DELETE') ® DECTRIS ARINA User Manual v1.8.1 18 | 29... -
Page 23: Trigger Usage Introduction
In order to record an image or a series of images, the ARINA detector has to be initialized, configured, armed, and the exposure(s) started by a trigger signal. The steps necessary to record an image series are compre- hensively described in chapter 5 and section 7.2. -
Page 24: Inte - Internal (Software) Enable
| command | arm detector | command | trigger {”value”: 0.7} As the trigger command is sent over an TCP/IP connection the exact latency of the start of the exposure is hard to predict. ® DECTRIS ARINA User Manual v1.8.1 20 | 29... -
Page 25: Exts - Externally Triggered Exposure Series
Consult the Technical Specifications for details about the required electrical characteristics of the trigger signal. The ARINA detector systems also support external triggering. In the trigger_mode ’exts’, nimages are recorded per trigger until ntrigger are received. Both count_time as well as frame_time are defined by the configuration. -
Page 26: Exte - Externally Enabled Exposure Series
The ARINA detector systems also support external enabling. In the external enable mode ’exte’ a series of ntrig- ger frames can be recorded. The count time as well as the period of individual frames of a series are defined by the duration of the high state of the external enable signal. - Page 27 Figure 8.4 illustrates a externally enabled series. nimages frame_time count_time Enable Out External In Time Figure 8.4: Exposures defined by external enable ® DECTRIS ARINA User Manual v1.8.1 23 | 29...
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Page 28: Pixel Mask
9.2. Updating the pixel mask 9.2.1. Overview Updating the pixel mask of a ARINA detector system involves four basic steps: 1. Retrieving the current pixel mask from the detector system via the SIMPLON API. 2. Manipulating the pixel mask to add or update pixels. -
Page 29: Uploading And Storing The Pixel Mask
# Set a new noisy pixel [y,x] pixelMask[234, 123] = 8 # Upload the updated pixel mask maskClient.setMask(pixelMask, 'pixel_mask') # Ensure that you 'arm' the detector to save the new pixel masks persistently ® DECTRIS ARINA User Manual v1.8.1 25 | 29... -
Page 30: Flatfield
10.2. Creating a flatfield 10.2.1. Overview Creating a custom flatfield for the ARINA detector system involves two basic steps: 1. Acquire uniformly-illuminated image via the SIMPLON API. 2. Upload pixel-wise correction factors via the SIMPLON API. -
Page 31: Upload Pixel-Wise Correction Factors
Uploaded flatfields are lost after (re-)initializing the detector or changing configuration param- eters like e.g. incident_energy or counting_mode. The following Python code demonstrate how to update the correction factors on the DCU with the DMaskClient from section 9.2: ® DECTRIS ARINA User Manual v1.8.1 27 | 29... - Page 32 # read image with homogeneous illumination (> 100,000 counts per pixel) dataFlatfield = tifffile.imread('flatfield.tif') # Calculate pixel−wise correction factors dataFlatfield = numpy.median(dataFlatfield) / dataFlatfield.astype('float32') # Upload pixel−wise correction factors maskClient.setMask(dataFlatfield, 'flatfield') # ... continue with the acquisition ® DECTRIS ARINA User Manual v1.8.1 28 | 29...
- Page 33 Trademarks ® Registered trademarks ”DECTRIS”: AU, AUS, CH, CN, DE, FR, IT, JP, KR, USA, UK, ”DETECTING THE FUTURE”: AUS, CH, CN, EU, JP, KR, USA, UK, ”DECTRIS INSTANT RETRIGGER”: AUS, CH, CN, EU, JP, KR, USA, UK ”Lines-ROI”: CH, EU, JP ”DECTRIS ELA”: AUS, CH, CN, EU, JP, KR, UK, USA...
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