ScanImage 2016 : Supported Microscope Hardware

Created by ed kang, last modified by bruce kimmel on Apr 19, 2018
Contents

Scanhead Hardware

ScanImage 2018 supports a wide variety of scanning systems including linear (galvo/galvo, GG) and resonant/galvo (RG) systems. Resonant scanning with multiple
regions of interest (MROI) is supported for GG and resonant/galvo/galvo (RGG) systems. Parallel scanning systems are supported to provide simultaneous imaging
and photostimulation. 

Supported scanning configurations can be ordered as a preassembled system, or as individual components.

Vendor 

Cambridge Technology & others

Acquisition and Control Hardware

Introduction

ScanImage 2015 and later allows users to configure their system for resonant scanning or linear scanning (=galvo only scanning). A microscope with two laser paths can combine both methods to allow for simultaneous imaging and photostimulation.

The sections below describe the basic acquisition and control hardware requirements for both imaging systems.

 

Resonant Scanning

ScanImage uses the National Instruments National Intruments FlexRIO platform for the core acquisition and control tasks for resonant two-photon laser scanning microscopy

ScanImage supports a handful of pre-specified FlexRIO system configurations

NI ScanImage Resonant Scanning Bundle

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Vidrio Technologies offers National Instruments hardware bundles, to help users create valid configurations. If you also order a ScanImage optimized computer from us at the same time, Vidrio will install ScanImage and create a custom machine data file for your system.

Email us at support@vidriotech.com for a ScanImage hardware bundle quote.

(info) See notes below for further information about the key options

Configuration Guide

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Please see Configuring ResScan (Resonant Scanning) page for additional details. 

Required

RoleItem(s)Performance characteristics
Chassis/controllerPXIe-1073 or better 
Scan Control DAQPXIe-6341NI PXI-based X Series DAQ
Digitizer

One of

NI Digitizer Module

  • 2 channel
  • 4 channel
FPGA Module

One of

NI PXI-based FlexRIO Module

  • Basic option
  • Performance option

For SI5 - there will be no difference in operation. Most users should order the PXIe-7961R.

Future versions may utilize the far greater (~10x) processing power of the PXIe-7975R.
The 7975R has been supported by SI5 since Fall 2014

Optional

Additional X Series multifunction DAQ boards for some features:

PurposeOptionsNotes
Pockels controlPCIe-6321 or PXIe-6341Highly recommended - allows blanking laser during resonant scanner slowdown and galvo scanner flyback
Piezo/Fast Z controlPCIe-6321 or PXIe-6341Allows for volume imaging applications
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The PXIe option is moderately more expensive, but has some advantages:

  1. Simplifies wiring complexity between boards.
  2. Reduces the number of PCIe slots required in the computer (or makes more available).

Linear Scanning

ScanImage uses National Instruments Multifunction DAQ boards for image acquisition and microscope control.

Recommended hardware

RoleItem(s)Notes

PMT acquisition, galvo control

NI-6356

 For multi-PMT acquisition, a simultaneously sampled NI X-series board is required.

Optional

RoleItem(s)Notes
Pockels controlPCIe/PXIe-6341Highly recommended - allows blanking laser during resonant scanner slowdown and galvo scanner flyback
Piezo/FastZ controlPCIe/PXIe-6341Allows for volume imaging applications
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Users upgrading from ScanImage 3.8 can reuse their existing PCI-6110/6132/6133 digitizers, but will need to purchase at least one additional X-series board (e.g. PCIe-6321). Please contact us at support@vidriotech.com to learn about upgrade options from ScanImage 3.x

Configuration Guide

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Please see Configuring LinScan (Galvo Galvo scanning) page for additional details.

Preamplifier Hardware

Photomultiplier tubes require a transimpedance amplifier for recording by ScanImage.

The optimal bandwidth depends on the sample rate and shortest pixel durations. 

For resonant scanning a bandwidth of at least 30 Mhz is recommended.

The Femto DHCPA-100 is a commercial off-the-shelf option suited for ScanImage 5 and later, at its 80MHz setting.

Thorlabs also makes a usable transimpedance amplifier. Please contact them directly for a part number and quote.

Computer Hardware

 

 Minimum Recommended
CPU

64-bit processor with at least 4 cores, ≥ 2GHz

Examples:

  • All Intel 3'rd gen (Ivy Bridge) Core i5/i7 systems (except i5-3470T)
  • All Intel Intel 4'th gen (Haswell) Core i5/i7 systems (except i5-4570T/TE)
  • Xeon E5-2609 or E5-2620

(info) Processors/systems with at least 6 cores may be valuable for future ScanImage or user-specific requirements combining TPLSM imaging with other simultaneous processing/acquisition

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Matlab is single threaded in its base configuration, so that a high CPU clock rate is desirable.

RAM

≥ 8 GB RAM

(info) Additional RAM may be valuable for future ScanImage or user-specific requirements, e.g. online image analysis done in User Functions 

PCIe slots
  • (usually) PCIe x16 for a graphics card.
  • (required) PCIe x1 for MXI controller connecting to the PXI chassis
  • (optional) PCIe x1 for a PCIe-6321 dedicated to Pockels control
  • (optional) PCIe x1 for a PCIe-6321 dedicated to Piezo/Fast Z control.

(info) If PXIe based DAQ's (e.g. PXIe-6341) for Beams and Fast Z features, then the PCIe slot requirements are reduced accordingly. Only the PCIe x1 slot for the MXI controller card is strictly required.

(info) Additional PCIe slots may be valuable for future ScanImage or other user-specific requirements

Hard Drives

A separate drive or partition for OS and data logging/storage is recommended, to avoid contention

Either a RAID 0 magnetic drive pair or solid-state drive (SSD), whole or partition, is recommended for data logging/storage, to achieve high performance.

Examples:

  • Drive for OS plus separate solid-state drive (SSD) for data logging/storage

OR

  • Single solid-state drive (SSD) of 500GB or higher, with separate partitions for OS & data storage

OR

  • Drive for OS plus separate magnetic RAID 0 drive pair
OS
  • Windows 7 Professional
  • Windows 8.1 Professional
  • Windows 10 Professional

 

Piezo Hardware (Optional)

VendorControllerCompatible PiezosComments
Physik Instrumente

E-665
E-709 (CHG)
E-753

PIFOC piezos (e.g. P-721, P-725, P-725.xDD, P-725KHDS) 
nPointLC.40xnPFocus objectivesOptions from 100um to 1000um of travel
Generic  Any focusing device accepting a -10V..10V analog command signal.

 

Stage Hardware (Optional)

VendorStage ControllersSI 5.2SI2016
SutterMP-285, MPC-200(tick)(tick)
TholabsMCM3000, MCM5000, MCM6000, Bergamo II Scope(tick)(tick)
Scientifica

Patchstar (2), Slice Scope
UMS (2), MMTP. MMSP, MMBP, IMTP

(tick)(tick)
Physik InstrumenteE-665, E-709 (CHG), E-753, C-884, C-863(tick)(tick)
nPointLC.400 Series(tick)(tick)
Newport*XPS(tick)(tick)
GalilDMC 4040 (tick)
Luigs & NeumannSM5, SM7 (tick)
PriorProScan III (tick)

*Requires MATLAB Instrument Control Toolbox

 

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