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{} {
Wiki Markup
Composition Setup
 Table of Contents
...
maxLevel
...
5
New Features in ScanImage 3.7
...
  • Compatibility 
...
  •  with 
...
  •  latest 
...
  •  Matlab 
...
  •  (2010b) 
...
  •  and 
...
...
...
  • .
  • Compatibility with X series boards, for the second DAQ board (for Pockels and/or more clock signals)
  • DAQ Toolbox no longer required
  • Automatic power adjustment during stack collection
  • Exports line/frame/pixel 
...
  •  clock 
...
  •  signals
...
  • Next 
...
  •  Triggering
...
  •  feature
...
  • Continuous 
...
  •  file 
...
  •  streaming 
...
  •  supported 
...
  •  for 
...
  •  stacks
...
  • Enhanced 
...
  • User 
...
  •  Functions
...
  •  capability
...
  • Enhanced 
...
  • Fast 
...
  • Configurations
Upgrading from ScanImage 3.5 
...
 or 
...
 3.6
...
  • 3.7 
...
  •  has 
...
  •  a 
...
...
...
...
...
  •  , 
...
  •  which 
...
  •  is 
...
  •  quite 
...
  •  thoroughly 
...
  •  documented. 
...
  •  You 
...
  •  should 
...
  •  make 
...
  •  a 
...
  •  new 
...
  •  standard.INI 
...
  •  file 
...
  •  based 
...
  •  on 
...
  •  this 
...
  •  model, 
...
  •  following 
...
  •  the 
...
  •  comments.
...

  •  (tick) It is recommended to create a separate folder(s) 
...
  •  for 
...
  •  your 
...
  •  INI/CFG/USR 
...
  •  files 
...
  •  under 
...
  •  3.7, 
...
  •  to 
...
  •  keep 
...
  •  them 
...
  •  separate 
...
  •  from 
...
  •  data 
...
  •  files 
...
  •  for 
...
  •  any 
...
  •  older 
...
  •  version 
...
  •  you 
...
  •  may 
...
  •  also 
...
  •  maintain 
...
  •  installed. 
...
  • The Shift and Scan Amplitude values that previously referred to X/Y 
...
  •  now 
...
  •  refer 
...
  •  to 
...
  •  Fast/Slow. 
...
  •  A 
...
  •  new 
...
  •  control 
...
  •  in 
...
  • Configuration
...
  •  dialog 
...
  •  indicates 
...
  •  mapping 
...
  •  from 
...
  •  X/Y 
...
  •  to 
...
  •  Fast/Slow 
...
  •  axes. 
...
  •  Adjusting 
...
  •  this 
...
  •  allows 
...
  •  you 
...
  •  to 
...
  •  rotate 
...
  •  the 
...
  •  image 
...
  •  90 
...
  •  degrees.
...

  •  (info) The INI file contains the separate mapping of X/Y 
...
  •  to 
...
  •  DA 
...
  •  Channels 
...
  •  0 
...
  •  & 
...
  •  1, 
...
  •  which 
...
  •  is 
...
  •  fixed 
...
  •  on 
...
  •  initialization. 
...
  • The Scan Amplitude values are replaced by Scan Angular Range values, in the Configuration dialog. It now represents the full (peak-peak) 
...
  •  angle 
...
  •  of 
...
  •  the 
...
  •  scan 
...
  •  range, 
...
  •  specified 
...
  •  in 
...
  •  optical 
...
  •  degrees, 
...
  •  rather 
...
  •  than 
...
  • half
...
  •  angle 
...
  •  as 
...
  •  in 
...
  •  3.6 
...
  •  (and 
...
  •  earlier 
...
  •  verisions). 
...
  •  Therefore 
...
  •  new 
...
  •  values 
...
  •  will 
...
  •  generally 
...
  •  be 
...
  • twice
...
  •  the 
...
  • Scan 
...
  •  Amplitude
...
  •  values 
...
  •  in 
...
  •  ScanImage 
...
  •  3.6/3.5.
...

  •  (info) The model INI file has improved/expanded 
...
  •  the 
...
  •  explanation 
...
  •  of 
...
  •  the 
...
  • voltsPerOpticalDegree
...
  •  variable. 
...
  •  Please 
...
  •  read 
...
  •  carefully, 
...
  •  and 
...
  •  provide 
...
  •  feedback 
...
  •  if 
...
  •  this 
...
  •  is 
...
  •  not 
...
  •  clear! 
...

  •  (warning) If the voltsPerOpticalDegree value in 3.7 
...
  •  differs 
...
  •  compared 
...
  •  to 
...
  •  your 
...
  •  setting 
...
  •  in 
...
  •  3.6 
...
  •  (i.e. 
...
  •  because 
...
  •  it's 
...
  •  clearer 
...
  •  now 
...
  •  and 
...
  •  therefore 
...
  •  set 
...
  •  correctly), 
...
  •  you 
...
  •  will 
...
  •  need 
...
  •  to 
...
  •  further 
...
  •  adjust 
...
  •  your 
...
  • Scan 
...
  •  Angular 
...
  •  Range
...
  •  values 
...
  •  compared 
...
  •  to 
...
  •  previous 
...
  • Scan 
...
  •  Amplitude
...
  •  values.
...

  •  (tick) In general, 
...
  •  the 
...
  •  new 
...
  •  default 
...
  • Scan 
...
  •  Angular 
...
  •  Range
...
  •  value 
...
  •  of 
...
  •  15 
...
  •  should 
...
  •  not 
...
  •  often 
...
  •  require 
...
  •  modification 
...
  •  by 
...
  •  most 
...
  •  users. 
...
  •  If 
...
  •  you 
...
  •  see 
...
  •  the 
...
  •  field-of-view 
...
  •  is 
...
  •  different 
...
  •  (smaller) 
...
  •  than 
...
  •  you're 
...
  •  used 
...
  •  to, 
...
  •  look 
...
  •  closely 
...
  •  at 
...
  •  the 
...
  • voltsPerOpticalDegree
...
  •  value/notes 
...
  •  in 
...
  •  the 
...
  •  INI 
...
  •  file.
...
  • It 
...
  •  is 
...
  •  recommended 
...
  •  to 
...
  •  copy 
...
  •  your 
...
  •  old 
...
  •  CFG 
...
  •  files 
...
  •  to 
...
  •  a 
...
  •  separate 
...
  •  folder 
...
  •  for 
...
  •  3.7, 
...
  •  and 
...
  •  then 
...
  •  load 
...
  •  and 
...
  •  re-save 
...
  •  each 
...
  •  of 
...
  •  them 
...
  •  individually. 
...
  •  This 
...
  •  will 
...
  •  make 
...
  •  your 
...
  •  CFG 
...
  •  files 
...
  •  3.7 
...
  •  compatible.
...

  •  (warning) Note the ScanAmplitude values will not be applied in 3.7. 
...
  •  The 
...
  • Scan 
...
  •  Angular 
...
  •  Range
...
  •  values 
...
  •  should 
...
  •  be 
...
  •  adjusted 
...
  •  before 
...
  •  saving 
...
  •  each 
...
  •  CFG 
...
  •  file. 
...
  • 3.7 
...
  •  requires 
...
  •  the 
...
...
...
  •  between 
...
  •  boards 
...
  •  (main 
...
  •  board 
...
  •  and 
...
  •  Pockels) 
...
  •  be 
...
  •  on 
...
  • RTSI 
...
  •  7
...
  • , 
...
  •  not 
...
  • RTSI 
...
  •  6
...
  •  as 
...
  •  with 
...
  •  ScanImage 
...
  •  3.6.
...

  •  (tick) If running both 3.6 
...
  •  & 
...
  •  3.7, 
...
  •  you 
...
  •  should 
...
  •  connect 
...
  •  both 
...
  • RTSI 
...
  •  6
...
  •  and 
...
  • RTSI 
...
  •  7
...
  • (or 
...
  •  connect 
...
  •  all, 
...
  •  with 
...
  •  a 
...
  •  ribbon 
...
  •  cable).
...

  •  (tick) If running both 3.5 
...
  •  & 
...
  •  3.7, 
...
  •  no 
...
  •  change 
...
  •  is 
...
  •  required
...
  • You can run 3.7 
...
  •  on 
...
  •  same 
...
  •  machine 
...
  •  that 
...
  •  is 
...
  •  running 
...
  •  3.6 
...
  •  or 
...
  •  older 
...
  • version
     (tick) Typically, 
...
  •  your 
...
  •  newer 
...
  •  Matlab 
...
  •  will 
...
  •  set 
...
  •  path 
...
  •  to 
...
  •  3.7 
...
  •  and 
...
  •  older 
...
  •  Matlab 
...
  •  will 
...
  •  set 
...
  •  path 
...
  •  to 
...
  •  older 
...
  • version
     (tick) If running both 3.5/3.6 
...
  •  & 
...
  •  3.7 
...
  •  on 
...
  •  same 
...
  •  machine, 
...
...
...
  •  is 
...
  •  required. 
...
  •  This 
...
  •  is 
...
  •  earliest 
...
  •  version 
...
  •  of 
...
  •  DAQmx 
...
  •  supported 
...
  •  by 
...
  •  3.7, 
...
  •  while 
...
  •  3.5/3.6 
...
  •  doesn't 
...
  •  run 
...
  •  on 
...
  •  8.9 
...
  •  or 
...
  •  higher. 
...

  •  (info) Note that X series boards are only supported from 9.0 
...
  •  forward.
...
Guide to New Features
Frame/Line/Pixel 
...
 Clock 
...
 Export


{
 Tip
}
This 
 
 feature 
 
 is 
 
 most 
 
 powerful 
 
 with 
 
 new 
 [
X 
 
 series 
 
 boards
|http://www.ni
. 
com/xseries/]. 
 Future 
 
 ScanImage 
 
 versions 
 
 may 
 
 be 
 
 able 
 
 to 
 
 get 
 
 more 
 
 functionality 
 
 out 
 
 of 
 
 other/earlier 
 
 board 
 
 families, 
 
 but 
 
 this 
 
 cannot 
 
 be 
 
 guaranteed 
 
 as 
 
 a 
 
 development 
 
 priority.
{tip}

* Each clock output requires a National Instruments [
...
...
  • . 
...
  •  These 
...
  •  must 
...
  •  be 
...
  •  specified 
...
  •  in 
...
  •  the 
...
  •  INI 
...
  •  file 
...
  • – frameClockBoardID
...
  • , 
...
  • frameClockCtrID
...
  • , 
...
  • lineClockBoardID
...
  • , 
...
  •  etc.
...

  •  (info) Note that Ctr0 on the primary board (acquisitionBoardID) is reserved by ScanImage, and not available for frame/line/pixel 
...
...
  •  channels, 
...
  •  while 
...
  •  other 
...
  •  board 
...
  •  families 
...
  •  have 
...
  •  only 
...
  •  2 
...
  •  counter/timer 
...
  •  channels
...
  • Finite 
...
  •  clock 
...
  •  generation 
...
  •  is 
...
  •  only 
...
  •  possible 
...
  •  with 
...
...
...
...
  • . 
...
  •  When 
...
  •  using 
...
  •  a 
...
  •  non-X 
...
  •  series 
...
  •  board, 
...
  •  additional 
...
  •  clock 
...
  •  'ticks' 
...
  •  may 
...
  •  appear 
...
  •  after 
...
  •  acquisition 
...
  •  is 
...
  •  finished, 
...
  •  because 
...
  •  the 
...
  •  counter 
...
  •  output 
...
  •  is 
...
  •  actually 
...
  •  stopped 
...
  •  in 
...
  •  software.
...
  • Consequently, 
...
  •  pixel 
...
  •  clock 
...
  •  generation 
...
  • – which 
...
  •  requires 
...
  •  finite 
...
  •  clock 
...
  •  generation 
...
  • – is 
...
  •  only 
...
  •  possible 
...
  •  with 
...
...
...
...
  •  at 
...
  •  this 
...
  •  time.
...
  • For 
...
  •  Frame/Line 
...
  •  clocks, 
...
  •  the 
...
  •  edge 
...
  • not
...
  •  specified 
...
  •  by 
...
  • Polarity
...
  •  signifies 
...
  •  the 
...
  •  end 
...
  •  of 
...
  •  Frame/Line. 
...
  •  For 
...
  •  Pixel 
...
  •  clock, 
...
  •  the 
...
  •  edge 
...
  • not
...
  •  specified 
...
  •  by 
...
  • Polarity
...
  •  is 
...
  •  controlled 
...
  •  by 
...
  • Pixel 
...
  •  Fraction
...
  • .
     (info) The 'end' 
...
  •  of 
...
  •  Frame/Line 
...
  •  indicates 
...
  •  that 
...
  •  acquisition 
...
  •  has 
...
  •  ended 
...
  •  for 
...
  •  current 
...
  •  line/frame, 
...
  •  and 
...
  •  acquisition 
...
  •  for 
...
  •  new 
...
  •  line/frame 
...
  •  has 
...
  •  not 
...
  •  begun. 
...
  •  This 
...
  •  occurs 
...
  •  at 
...
  •  the 
...
  •  scanner 
...
  •  flyback 
...
  •  or 
...
  •  turnaround 
...
  •  time 
...
  •  at 
...
  •  end 
...
  •  of 
...
  •  line, 
...
  •  or 
...
  •  end 
...
  •  of 
...
  •  last 
...
  •  line 
...
  •  in 
...
  •  frame.
     (info) The Pixel clock handling is different because there are no gaps between pixel periods; thus the location of the 'stop' edge must be user specified (via Pixel Fraction).
 Panel
 Wiki Markup



(i) The Pixel clock handling is different because there are no gaps between pixel periods; thus the location of the 'stop' edge must be user specified (via *Pixel Fraction*).


{center}!ExportedClocks.bmp!{center}

* *Enable*: Each clock can be enabled/disabled. (*CFG* setting)
* *Phase Shift (us)*: Each clock signal can be phase shifted relative to the true start of frame/line/pixel. Only a positive phase shift (delay) is supported at this time. (*CFG* setting)
* *Polarity*: Specifies if rising or falling edge signals the start of frame/line/pixel.
* *Pixel Fraction*: Specifies at what fraction of the pixel period to generate the edge _not_ specified by the *Polarity*. Value must be < 1, to allow edge specified by *Polarity* at start of subsequent pixel period. (*CFG* setting)

* *Export Clocks on FOCUS*: If false, the clock signals are only generated during *GRAB/LOOP* acquisitions, not *FOCUS* acquisitions. (*USR* setting)




(/) Settings labeled as *CFG* settings are saved as part of ScanImage [Configuration|http://openwiki.janelia.org/wiki/pages/viewpage.action?pageId=8684238]. Different configuration files can save different values of this setting. This is useful, for instance, if you want the frame clock to be exported only for certain experiments, but not others. 


* The pixel clock capability is only available with [X series boards|http://www.ni.com/xseries/] support finite output

* 


h4. _Next Triggering_ Feature
*& _Next Triggering_ allows external trigger 
Next Triggering Feature
*& Next Triggering allows external trigger (e.g. 
...
 from 
...
 behavior 
...
 apparatus) 
...
 to 
...
 stop 
...
 an 
...
 acquisition, 
...
 or 
...
 to 
...
 start 
...
 a 
...
 new 
...
 file 
...
 with 
...
 advanced 
...
 number 
...
 without 
...
 stopping 
...
 acquisition
...
Power 
...
 Adjustment 
...
 During 
...
 Stacks
...
  • based 
...
  •  on 
...
  •  configurable/measurable 
...
  •  length 
...
  •  constant
...
Continuous 
...
 File 
...
 Streaming 
...
 Improvements
...
  • Continuous 
...
  •  file 
...
  •  streaming 
...
  •  is 
...
  •  now 
...
  •  supported 
...
  •  for 
...
  •  stacks
...
  • Continuous 
...
  •  file 
...
  •  streaming 
...
  •  is 
...
  •  now 
...
  •  the 
...
  •  only 
...
  •  mode. 
...
  •  A 
...
  •  configurable 
...
  •  running 
...
  •  data 
...
  •  buffer 
...
  •  is 
...
  •  maintained 
...
  •  still, 
...
  •  for 
...
  •  online 
...
  •  processing 
...
  •  needs.
...
Enhanced 
...
 User 
...
 Functions 
...
 capability
...
  • Numerous 
...
  •  events 
...
  •  to 
...
  •  which 
...
  •  user 
...
  •  functions, 
...
  •  with 
...
  •  optional 
...
  •  modulating 
...
  •  arguments, 
...
  •  can 
...
  •  be 
...
  •  bound.
...
DAQ Toolbox No Longer Required
  • - instead uses a Matlab class which wraps the NI DAQmx library. This approach is faster and more comprehensive (e.g. 
...
  •  allows 
...
  •  access 
...
  •  to 
...
...
  •  features)
...