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1.1 What is it?

This software is aimed to record optical data and electrophysiological data simultaneously for physiological experiments. Of course, optical recording (usually a CCD camera is used) or electrophysiological recording can be performed separately. On-line acquisition and off-line analysis can be performed on this single application. Off-line analysis is also capable on data files produced by some kinds of other acquisition software. Off-line analysis can be performed in combination with other applications (e.g., Igor Pro, ImageJ or Exel) by automatic data transfer mechanisms.

1.2 What you need.

1.2.1 Hardware

• Computer

  TI Workbench (TIWB) works on Intel Macs running OS X 10.6 or later.

• Slave Windows PC

  Some cameras and I/O interfaces connected to a Windows PC can be used by TI Workbench through network connection. Or Windows running in a virtual environment on the host Mac can be used for this purpose. By this way, devices which are not supported for Mac can be used by TI Workbench running on a Mac.

  Notes to use a Windows PC as a device driver.

  • Ask the author of TIWB to compile a version of TIWB for this purpose.

    The computer name of Windows PC, which is displayed through the "system property" of the "Control Panel" of the Windows PC, is useful.
    

  • Firewall of the windows PC must be turned off.
  • In case for Windows PC running in VirtualBox on the host Mac:
    • In the network setting of VirtualBox choose "host only adapter". The default network configuration in VirtualBox may be "NAT" or "Bridge", which enable connecting the guest OS to the real Internet. So the tiwb on the host Mac and the winslave program on the virtual Windows communicate each other through a real Internet connection. If the real internet outside the host Mac is busy, the communication between the guest windows and mac is also slowed. With the “Host only adapter” option, the network connection is closed within the host Mac.
      To enable the "Host only adapter", a host network adapter must be created in a window which is opened via the "File"menu of VirtualBox menu -> "Host network manager".
      The computer name should appear in the host Mac’s network PC list. If not, run the "command prompt" program of Windows, type "ipconfig" and return, then read the IPv4 address (four digits separated by dots).
      
    • If the target device is connected through USB, connect the device to the host Mac, and register the device in the Port setting of VirtualBox. Select the USB tab, activate the “activate USB controller” check box, and add a device filter for the device.
  • Install a device driver software for the device in the Windows PC, if necessary.
  • Copy a “winslave.exe" file provided by the author to the Windows PC and run it.

    "winslave.exe" must be compiled for each device.

  • A console window (black background) should appear. IP addresses of the Windows PC are shown.
    
  • Run TIWB on the host Mac. If an IP address is asked to input, enter the IP address shown in the console window in the Windows PC.
    
  • The console window of “winslave.exe” should respond and some lines of text will be added.
• Camera

  More than a single type of camera can be used at the same time. For example, a video-rate CCD camera is used for real-time monitoring, and another scientific-grade digital CCD is used for fast time-lapse image acquisition.

  • Hamamatsu Photonics cameras
    • ORCA-ER
      • with Phoenix frame grabber (DataCell).
      • with Snapper DIG16 frame grabber (DataCell).
    • ORCA-ERG connected through FireWire: OS-X.
    • ORCA-R2 and IMagEM are supported.

    Firewire cameras with DCAM are supported on OS X 10.6-10.11. Cameras with USB interface can be used with VirtualBox and Windows (see above "Slave Windows PC"). And also Cameras connected to a real Windows PC can be also used with TIWB running on a Mac with Ethernet connection. ORCA Flash has been tested.
    

  • QImaging QCam cameras

    Although the QImaging states that the final QCam Mac Driver 2.0.10 works on OS X 10.6 - 10.11.

  • QImaging cameras with PVCAM
  • Although newer cameras from QImaging works only with PVCAM on Windows, cameras with USB interface can be used with VirtualBox and Windows. And also Cameras connected to a real Windows PC can be also used with TIWB running on a Mac with Ethernet connection.  QImaging Retiga ELECTRO has been confirmed to work by this way (see above "Slave Windows PC").
    
  • AVT Prosilica cameras (giga-bit Ether and Firewire)
  • When a giga-bit camera is used, follow below:
  • A route for 255.255.255.255 may need to be added to point to the adapter on which the camera will be plugged (or to the switch on which the camera will be). This can be done with the following command:
    
      > sudo route -n add 255.255.255.255 169.254.42.97
    
    where 169.254.42.97 is the IP (self-assigned or assigned by you) of the adapter.
  • If a second Ethernet port of a host Mac is used exclusively with an Ethernet-connected camera, the setting of the port in the network config panel is..
        IP address: 169.254.1.1
        subnet mask: 255.255.0.0
        router: leave empty
        DNS server: leave empty
    
  • Firewire cameras supported by libDC1394
    • libDC1394 web site
    • supported camera list
  • Photometrics (Roper) cooled CCD cameras driven by PVCAM library (32 bit only, OS X 10.5 - 10.13).
  • Scion Firewire cameras (the company has gone)
• A/D, D/A card
  • Instrutech ITC-16 and ITC-18 (Nubus, PCI bus or USB) [web site]

    Latest ITC driver works with 64 bit TIWB.

    ITC-16 and ITC-18 connected to a real Windows PC can be also used with TIWB running on a Mac with Ethernet connection. It is useful for ITC devices of PCI connection.

  • National Instruments
    • NI PCIe-6259 and PCIe-6363: for Mac Pro. a special device driver ("Speedy") is necessary.
    • NI USB-6211:
      • Connect pin 1 (PFI0) and pin 6 (P1.0). It is necessary to synchronize AD and DA.
      • Use NIDAQmxbase 3.7 for OS X 10.7 and 10.8. (TIWB crashes with NIDAQmxbase 3.6).

    NI devices connected to a real Windows PC can be also used with TIWB running on a Mac with Ethernet connection (see above "Slave Windows PC").

• Filter exchanger / Shutter
  • Olympus OXP-EXA with Service USB control 
  • Sutter Lambda 10-2 and DG-4 through serial connection. [web site]
  • TILL Polychrome monochromator with analog voltage control or serial port control.
  • Mac2000/5000 (Ludl) through serial control.
  • Uniblitz shutter connected through a serial port of a Macintosh or through TTL I/O.
• Microscope control
  
  • Olympus IX81 microscope can be controlled through a serial port (IX2-UCB-2 control box)

    supported devices:

    • Auto focus control unit (IX81-ZDC)
    • Motor driven mirror unit cassete (IX2-RFACA)
    • Disk Confocal Unit (IX2-DSU) (control of insert/remove of the confocal disk)
  • PI piezo Z-Drive is supported for z-sectioning.
• Wiring
  • Serial port communication on no-serial port Macintosh.

    Number of peripheral devices are controlled through the serial port. Keyspan's serial-USB adapter can be used to connect serial ports of devices and a USB port of a Macintosh.

  • TILL Polychrome monochromator
    • Control through serial port

      Serial port is optional for Polychrome-II/IV. Connect the first port of the serial ports of Macintosh (try the other port in case for no response) and serial port of Polychrome. Use a cross cable. Calibration of Polychrome is needed at the first time through the "config" dialog which can be activated by pressing the "config" button at the rigth top corner of the "CCD online" window.

    • Control through Master-8

      Connect Master-8 and Mac with serial cable.  A Keyspan USB-serial adaptor is also necessary on the Mac side.  On the Master-8 side a DB25 connector is necessary.  If you make a serial cable, refer to the Master-8 manual for wiring.  Connect the "4+5" BNC to the TILL analog input port.  Turn off the "=>" switch and turn on the "<=" switche on the Master-8 panel.  Set analog voltage for dark to channel 4 of Master-8, F1 to channel 5, F2 to channel 6, Ext1 to channel 7, and Ext2 to channel 8 by adjusting the thum turn dials and the +/- switches on the Master-8 panel.  If a CCD exposure trigger is further given from Master-8, use channel 2 of Master-8 for the trigger signal.
      

    • LabJack

      LabJack U3 can be used for controlling Master-8.  An x2 amplifier is necessary to expand the analog voltage from LabJack.
      

    • Control through electrophysiology stimulator (ITC-16, ITC-18, etc.)

      Connect one of output ports to TILL Polychrome analog command input, and set D/A port number in the filter configuration dialog. In this way control and recording of electrophysiology is not independent of timing control of Polychrome.
      

      This connection only applies for frame-transfer type cameras. This combination enables alternate filter mode in the fast continuous mode as well as the "negative delay" function. In addition to the required connections for (Polychrome-PCI-1200) and (camera-PCI-1200) described above, connect OUTB1 (pin 43) and EXTUPDATE (pin 39) of PCI-1200.

  • Princeton MicroMax series and ITC-18

    If "Start ITC-18 by READY trigger from MicroMax" option is used, connect "READY" out of MicroMax control box and external trigger input of ITC-18.

  • Sutter Lambda10-2 filter/shutter controller

    A special serial cable is necessary. Here is a connector assignment.  An additional Uniblitz shutter can be used by serial connection through another port. See below for cable configuration for Uniblitz shutter.  Port can be selected in the "filter configuration dialog" dialog.

  • Sutter DG-4 filter exchanger

    The same type of a serial cable as is used for Sutter Lambda10-2 is needed.

  • Mac2000/5000 filter/shutter controller

    Use a Keyspan USB-serial adaptor to connect the serial port of Mac2000/5000.

  • Vincent Uniblitz shutter connected to a serial port of a Macintosh

    A serial cable is necessary to connect Uniblitz shutter controller with a Macintosh. Here is a connector assignment diagram.  Port can be chosen in the "filter configuration dialog" dialog.

• 32 or 64 bit mode.

  TI Workbench is supplied as a 32 bit or 64 bit modes according to the combined hardware drivers. 

  Some Mac computers boots with the 64-bit kernel mode in OS-X by default.  When TI Workbench works with devices, of which device drivers only work in 32-bit mode, it is necessary to boot in the 32-bit kernel mode by pressing '3' and '2' at booting and install device drivers and run TI Workbench.  There is another way to change the default booting kernel. http://support.apple.com/kb/HT3773 has gone. "sudo systemsetup -setkernelbootarchitecture x86_64" or "sudo systemsetup -setkernelbootarchitecture i386" in the terminal application works.
  

• Igor Pro

  TI Workbench has been intended to make use of Igor Pro software as a final data presentation tool. Electrical and optical data can be exported to Igor Pro. Users are strongly recommended to use Igor Pro ver. 2.0 or later with TI Workbench. Demo version of Igor Pro can be downloaded from WaveMetrics web site

• ITC-16 and ITC-18 (Instrutech)
  • device drivers have to be installed.
• Hamamatsu DCAM cameras (ORCA-ER, ORCA-R2, ImagEM...)

  A DCAM driver must be installed.

• Photometrics CCDs (Quantix, CoolSnap, Cascade, etc.)

  Install the PVCAM driver for OS-X according to the manufacturer's instructions.

• National Instruments A/D, D/A card

  Some types work with TIWB.

1.3 Menu Bar

1.3.1 Apple Menu

Program version, user identification, and hardware configuration are displayed by "about dialog".

1.3.2 File Menu

• New
  • Layout: a Layout window is created.
    
  • Labnote: a Labnote window is created.
  • Configured Image: a Configured Image is created.
    
• Open (shortcut: cmd+O)

  Readable files are listed. In the file select dialog, when a TIWB format file is selected, packet is listed in the dialog with comments. Packets can be chosen directly by selecting packets and press "Open" button or double-clicking.

• Close (shortcut: cmd+W)

If the active window is disposable, it is closed.

• Save as...

  Save to another file as TIWB format from a TIWB format file (image & electrophysiological data)

  Data segments to be saved can be chosen with a dialog. This function enables removing unnecessary data segments from a file (actually, making another copy of data file containing only necessary data segments).

  For image data, refer to "Save as" section in "Imaging".

• Duplicate

  Duplicates an active image or A/D sweep window. This operation is equivalent to opening the same data file twice.

• Import from Igor

  If Igor Pro holds valid waves, this program imports one of them as A/D data. Refer to "Import from Igor" section in "Electrophysiology.

• Export... submenu

  This item is used for saving data in the active window into a variety of format files or directly export data to other application programs. Exporting a text file of time course plot or Excel format files are supported.

• Export to Igor (short cut: cmd+E)

  By exporting various data types to Igor, in-depth analysis and creation of publish-quality figures are performed. Exporting image data set is explained here.

• Export to Excel
• Export to a PDF file
• "Export...": Exporting in other formats.
  

• Page Setup...

  Configures printer setting. This setting is applied to any printing functions in this program. If there is spooled A/D data, the user is asked to print or dispose it.

• Print (shortcut: cmd+P)

  Print contents in an active window. Image window and A/D sweep window use their own printing switches instead of this menu item.

• Update Preference file

  Update preference file (either in default preference folder, or user-specific preference file) is updated by the current parameters. Refer to the next section for the detail of the "preference file".

• Save Preference as...

  Preferences (e.g., image options, A/D options, CCD acquisition setting, stimulator setting, etc.) are saved as a preference file, which can be retrieved just by opening it (double clicking, through Open in this menu, or drag'n drop it to this program's icon). Parameters for on-line items (CCD setting, stimulator setting, etc.) are only retrieved if a preference file is opened at start-up time of this application, i.e., this application is started by dropping a preference file onto the application icon, or double clicking a preference file. Otherwise, preferences stored in the default preference file ("TI Workbench.pref") located in "preferences" folder in the system folder are retrieved, which was saved automatically at the exit time of the last session.

  Once a user starts the program with a user-specific preference file, all the settings and parameters are stored back into the user-specific file used at start-up instead of the default preference file. So users can have different setting files for different experiments. The rule is following.

  If tiwb is started with a preference file (by dropping a preference file onto tiwb icon or double-clicking a preference file icon), all the settings and parameters are stored back into the same preference file. The default preference file ("System folder"->"preferences"->"TI Workbench.pref") is not altered.

  Tiwb refuses to be started with more than one preference files.

  After starting tiwb, preference files can be opened by double clicking or droppiing their icons onto tiwb's icon to change (not all of) settings and parameters of the program. But, settings and parameters are stored back not to parameter files opend during execution but to the preference file read at starting time. 

* If a National Instruments NI-DAQMXbase driver is used, this "drag'n dropping preference file scheme" to use different parameter files can not be used.


• Quit (shortcut: cmd+Q)

  Quits this program.

1.3.3 Edit Menu

• Undo (shortcut: cmd+Z)
• Redo (shortcut: cmd+shift+Z)
• Cut (shortcut: cmd+X)
• Copy (shortcut: cmd+C)

  Copies data in the active window. Data can be in text or PICT format. For Image windows, this "Copy" operation not only copies a PICT image into clipboard which can be pasted in other applications but also copies several properties of the image into internal buffer which can then transfered to other image windows through "Paste Special" operation. This "copied properties" is held in the preference file, which can be recalled in the next program start-up time. Text data can also be drag'n dropped to other applications.

• Copy Special (shortcut: cmd+shift+C)

  For image window, copying LUT (color look up table) into clipboard as a PICT image is possible through this menu.

• Paste (shortcut: cmd+V)
• Paste special... and Paste special (shortcut:cmd+shift+V)

  For image windows, these paste (transfer) some of the properties recorded by the "Copy" operation.  "Paste special..." asks items to be pasted by displaying a dialog.  "Paste special" pastes items selected previously through "Paste special...".

• Clear
• Select All (shortcut: cmd+A)
• Note (shortcut: cmd+M)

  This command sends text information of the active data Window to the "Note" text window.

• Note Format...

  Format (tab, comma) and kind of information to be exported to the Note window can be chosen.

• PICT Format...

  Set format when contents of a Window is exported as a PICT data. This option is dependent to the type of the active window. This option affects the results of "Copy", "Layout", "Print" and some other cases (e.g., movie contents of image data through the "Save as..." menu). For PICT format of image data, refer to "PICT Format..." in the imaging section.
  
  

1.3.4 Layout Menu

The Layout Window is explained in "Layout Window" section in "Miscellaneous".

• Append

  This command sends a PICT image of the active window to the Layout Window.

• Zoom

  Changes the zoom factor of the Layout window. This does not change the actual size of the layout on print, but just changes the displayed size.

• to Front

  Sends selected items in the Layout Window to the front.

• to Back

  Sends selected items in the Layout Window to the back.

• align Left
• align Right
• align Top
• align Bottom

  These commands align selected items in the Layout Window.

• Horiz. regular interval
• Vert.regular interval

  These commands arrange the interval of the selected items in the Layout Window.

• options...

  Sets options for the Layout Window.

• Text Input (cmd + T)

  Put text in the layout.

1.3.5 Window Menu

Windows can be called back to the front using this menu.

1.3.6 Misc-Option Menu

• Warn on closing Log Window

  When closing the Log Window (pressing go away box in the window title, or quitting the application), an alert appears when this item is checked.

• Speech Recognition

  When Speech Recognition manager (a part of Mac OS) is installed, some of the functions can be ordered by voice. For detail refer here.

  
  

1.3.7 other Option Menus

Other options can be set through "ad-option" or "image-option" menu which appear on the Menu Bar when an A/D window or an image window is active.

1.4 Miscellaneous

1.4.1 Copy Protection

This program is protected from illegal copy by a copy protection mechanism. Only registered Macintoshes can perform on-line acquisition. On non-registered Macintoshes, file browsing (i.e., other than acquiring through a CCD camera or an A/D card) can be done. To know whether a Mac is registered or not, check the "about Dialog" from the Apple Menu.

1.4.2 slide text edit

Some text input fields in this application have an expanded function, "slide text edit". This allows modifying the value displayed in a text field box by sliding the mouse up and down. The cursor shape changes to an up-down arrow within a slide text edit box, which can be used for identifying a slide text edit box from ordinary text boxes.

When cursor shape changes to this (with a dot), alternative resolution can be chosen with the right mouse button (or mouse button with control key).

1.4.3 drag and drop operation

Drag and Drop operation is available by fetching the "Proxy Icon" in the window title (see figure) to Drag and Drop the PICT or TEXT information to other applications (Igor does not accept Drag and Drop, though).

Most of the editable text including the "Note" window can be drag'n dropped to other applications.

Drag'n drop the Proxy Icon of an Image window to another Image window results in overlaying the dropped image onto the destination Image window.

Drag'n drop onto Finder window or Desktop will create a PDF file.

1.4.4 file open

Data files can be opened by selecting "Open" in the File Menu of the Menu Bar, or by drag-and-drop data files over this application's icon. Data files created by this application can also be opened by double clicking them.

1.4.5 Log Window

Log window can be used as a notepad to input text using the keyboard. Information can also be sent to this window from image windows or electrophysiological data windows by selecting "Memo" in Edit menu (short cut: cmd + M) as text which can be copied and pasted to other applications. When this window is selected (active), text in this window can be saved to a text file by selecting "Save" and "Save As..." in the File Menu. Once the contents of the Note window is saved to a file, "Save" operation overwrites previously written file without warning overwrite. Saved file can be changed by selecting "Save As...".

Contents of the "Note" window" is also automatically stored in the current preference file (periodically saved). The contents is not erased by closing the window. At the moment, the contents must be manually erased (select all (cmd+A), then press delete key). The physical limit of the text length is 2 Mbytes (when exceeds, alert appears).

1.4.6 Layout window

The Layout windows are "paper sheet" where images and text can be placed and arranged.

• Image data can be placed in the Layout Window by using the "Copy" and "Paste" commands in the "Edit" menu (short cuts: cmd+C and cmd+V), or by selecting "append" in the "Layout" menu. The background of the Layout window shows the printable area at the current printer settings which is independent of the zoom factor selected for the Layout Window.
• Text can be placed and edited by double-clicking in the Layout window.
  
• Data on the Layout window can be copied to the clipboard and pasted to other application (e.g., Adobe Photoshop, Claris Draw). PICT data from other applications can be pasted from the clipboard into the TIWB Layout Window by "Paste" in the "Edit" menu (short cut: cmd+V).
• Many window types in tiwb support direct "drag and dropped" data transfer to the Layout window.
• External files in local Mac or files pointed by URL in the network can be also "drag and dropped" to layout windows. The original file is stored and indicated by a file name text.
  
• By double cricking this link, the stored file is opened. When the stored file includes image, image is appeared in the layout window.
  
• When an option key is pressed on drag'n drop, a link to the file is inserted to the layout window, which can be opened by double clicking the file image or file name text.
  
• When a HTML file is dropped from local disk or web browser, the content of web page is archived in the webArchive format which is stored in the Layout file data. If an option key is pressed during dropping a HTML file, the web page image is stored as an image, not a webArchive format, and URL is recorded.
• External file linkage and tiwb data linkage explained above are "loose link". Tiwb searches for the same file name in the same folder of the Layout file, then searches in the parent folder, child folders and child folders of the parent folder.
• Simple drawings (line, arrow, rectangle and circle) are placed from contextual menu (right click or click with control key in the window).
• Items in the Layout window can be selected by clicking. Several items can be selected by clicking with the shift key pressed. All items can be selected by "select all" in the "Edit" menu (short cut: cmd+A).
• "Collection" toolbar button opens a "collection" layout window, of which content is preserved over launching and quitting cycle. This window can be used to store frequently used elements (texts, arrows, etc.).
  
• Selected items can be moved by dragging with mouse.
• Selected items can be resized by dragging at the corners with mouse.
• Selected items can be removed from the Layout Window selecting "Cut" in the "Edit" menu (short cut: cmd+X) or by pressing the delete key.
• A selected item is expanded in a large window by pressing space key, which is hidden by pressing space key again, or pressing the "close" button of the popup window.
  
• The Layout Window can be printed by "Print" in the "File" menu (short cut: cmd + p).
• The Layout Window can be saved as a Layout format file by "Save as..." in the "File" menu .

Note: When multiple frames are sent to Layout Window, frames to be placed out of the window edge is wrapped and placed to a lower row. Thus, when the Layout Window width is narrow, number of frames in a column of frames is small.

1.4.7 Labnote window

The Labnote function was added to TIWB to realize an electronic laboratory note system, based on the "Layout" function (see above). The Labnote window/file holds the following functions in addition to the functions of Layout window/file described above.

• The file format of Labnote differs from that of layout. Layout can be converted to Labnote format by saving as Labnote format, but Labnote format file cannot be saved as "Layout" format file. Instead all the elements in a Labnote file should be copied and pasted to a new Layout window.
• Labnote format files are automatically saved every two minutes whenever changes have been added.
  

• Every element (text, image, drawings, etc.) in a Labnote window (file) holds time stamp. And each element is no longer be modified or deleted two weeks after addition to Labnote window/file. Still new elements can be added to Labnote window/files anytime.
• Whenever a labnote file is saved, a PDF format file is also created/renewed of the same name of the labnote file in the same folder. This assures that the content of labnote can be read in the future.
• Labnote window holds a directory side view. Upper part of side view shows directory structure and Labnote files, and Lower part of side view shows content of a folder selected in the upper part.

1.4.8 Online Help

Online Help is available for many dialogs and through "Help Menu" in the menu bar or pressing "help button" ('?') in dialogs.

OS-9 only: Balloon Help is available in some menus and dialogs in OS 9 or earlier versions of Mac OS.

1.4.9 AppleScript support

AppleScript example:

• example 1

  on open droppedItem tell application "TI Workbench" repeat with obj in droppedItem open obj export image 1 as tiff tiff format gray 8 close image 1 end repeat end tell end open

  If this AppleScript is saved as an executable file, dragging and dropping image files will produce 8 bit gray TIFF format files.

• example 2

  on open droppedItem tell application "TI Workbench" repeat with obj in droppedItem open obj export image 1 as movie codec H264 quality normal speed 100 close image 1 end repeat end tell end open

  If this AppleScript is saved as an executable file, dragging and dropping image files will produce QuickTime movies for every segment of a file with parameters H264 codec, normal quality and 100x speed.

• commands:
  • exportTIFF
    • direct object: format
      • "RGB8"(default), "native", "gray8", "index8", "gray16", "RGB16"
    • example
      • exportTIFF gray8
  • exportQTmovie
    • parameters
      • codec

        "H264" (default, recommended), "animation", "JPEG", motionJPEG"

      • quality

        "normal" (default), "low", "high", "max", "min", "lossless"

      • speed factor

        default: 1.0

      • "with all segments separated"

        if this phrase is added, movie files of all segments are created separately.

      • "with all segments combined"

        if this phrase is added, a movie file of all segments combined are created.

    • example

      exportQTmovie codec "H264" speed factor 10 with all segments separated

  • exportText
    • direct object: target plot

      "raw1", "raw2", "raw3", "raw4", "ratio", "ratioF2", "ratioF3", "atioF4", "ratioF3F4"

    • parameters
      • "with all segment"

        if this phrase is added, text files of all segments are created separately.

    • example

      exportText ratio with all segment

      exportText raw1

  • zoom
  • selectPlot
  • magnification
    • direct object: magnification factor (percent, integer)
    • example

      magnification 200

      this command set to 200% magnification of an image

  • ZCompress

Use Script Editor for scripting detail of TI Workbench, also.

1.4.10 Optional Key operations

In Image Windows

• shift key: to measure length / angle
• F1 key to measure movement of a particle through a stack of images.
• option key and ctrl key: to alter ROI position in each frame in a segment.
• left and right arrow keys
• without mofier keys: to move back/next image frame
• with shift key: change the active ROI instead of current frame
• with 'caps lock' key: track particle operation
  
• command key + right arrow key: start/stop fast animation.

1.4.11 Voice recognition

Some of the operations can be achieved by voice if a microphone is set (and Speech Recognition Manager is installed for OS-9). This feature can be turned on/off through the "Misc-Option menu" in the menu bar.

During sequential recording of images, voice recognition is turned off. And during A/D recordings, voice recognition except for "Stop" is
turned off.

1.4.12 Terminology

Some words are defined to clarify meaning in the program.

Interleave

The "Interleave" value determines number of segments to be skipped in the imaging session. "Interleave" can be set in two locations in the program, namely in the "link with oscillo" dialog and in the Segments section of the "ccd on line" dialog, allowing every (N+1)-th segment to be exposed and saved, respectively. Default value for interleave is zero, meaning that every imaging segment is being exposed and acquired.

Interval

"Interval" is the time between the start of one segment and the beginning of the next one, including the duration of the segment proper.

1.4.13 Citation

1. Hotta M, Hayase K, Kitanaka A, Li T, Takeoka S
   Development of the observation of membrane fusion with label-free liposomes by calcium imaging
   Biochem BioPhys Rep, 34:101483 (2023), doi:10.1016/j.bbrep.2023.101483
2. Li C, Saliba NB, Martin H, Losurdo NA, Kolahdouzan K, Siddiqui R, Medeiros1 D, Li W
   Purkinje cell dopaminergic inputs to astrocytes regulate cerebellar-dependent behavior
   Nat Commun, 14:1613 (2023), doi:10.1038/s41467-023-37319-w
3. Adachi C, Otsuka S, Inoue T
   Cholesterol-induced robust Ca oscillation in astrocytes required for survival and lipid droplet formation in high-cholesterol condition
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97. Tyler WJ, Pozzo-Miller L
    Miniature synaptic transmission and BDNF modulate dendritic spine growth and form in rat CA1 neurones
    J Physiol, 553:497-509 (2003)
98. Nakazawa T, Watabe AM, Tezuka T, Yoshida Y, Yokoyama K, Umemori H, Inoue A, Okabe S, Manabe T, Yamamoto T
    p250GAP, a novel brain-enriched GTPase-activating protein for rho family GTPases, is involved in the N-Methyl-D-aspartate receptor signaling
    Mol Biol Cell, 14:2921-2934 (2003)
    
99. Kuruma A, Inoue T, Mikoshiba K
    Dynamics of Ca²⁺ and Na⁺ in the dendrites of mouse cerebellar Purkinje cells evoked by parallel fibre stimulation
    Eur J Neurosci, 18:2677-2689 (2003), doi:10.1111/j.1460-9568.2003.02977.x
100. Fukami K, Yoshida M, Inoue T, Kurokawa M, Fissore RA, Yoshida N, Mikoshiba K, Takenawa T
     Phospholipase Cd4 is required for Ca²⁺ mobilization essential for acrosome reaction in sperm
     J Cell Biol, 161:79-88 (2003), doi:10.1083/jcb.200210057
101. McCutchen ME, Bramham CR, Pozzo-Miller LD
     Modulation of neuronal calcium signaling by neurotrophic factors
     Int J Dev Neurosci, 20:199-207 (2002)
102. Ivic L, Zhang C, Zhang X, Yoon SO, Firestein S
     Intracellular trafficking of a tagged and functional mammalian olfactory receptor
     J Neurobiol, 50: 56-68 (2002), doi:10.1002/neu.10016
103. Tyler WJ, Pozzo-Miller LD
     BDNF enhances quantal neurotransmitter release and increases the number of docked vesicles at the active zones of hippocampal excitatory synapses
     J Neurosci, 21:4249-4258 (2001)
104. Aihara Y, Inoue T, Tashiro T, Okamoto K, Komiya Y, Mikoshiba K
     Movement of endoplasmic reticulum in the living axon is distinct from other membranous vesicles in its rate, form, and sensitivity to microtubule inhibitors
     J Neurosci Res, 65:236-246 (2001)
105. Kume S, Saneyoshi T, Mikoshiba K
     Desensitization of IP₃-induced Ca²⁺ release by overexpression of a constitutively active Gqα protein converts ventral to dorsal fate in Xenopus early embryos
     Devlop Growth Differ, 42:327-335 (2001), doi:10.1046/j.1440-169x.2000.00519.x
106. Leonard CS, Rao SR, Inoue T
     Serotonergic inhibition of action potential evoked calcium transients in NOS-containing mesopontine cholinergic neurons
     J Neurophysiol, 84:1558-1572 (2000)
107. Kume S, Inoue T, Mikoshiba K
     Galphas family G proteins activate IP3-Ca²⁺ signaling via gbg and transduce ventralizing signals in Xenopus
     Dev Biol, 226:88-103 (2000), doi:10.1006/dbio.2000.9849
108. Pozzo-Miller LD,Gottschalk W, Zhang L, McDermott K, Du J, Gopalakrishnan R, Oho C, Sheng ZH, Lu B
     Impairments in High-Frequency Transmission, Synaptic Vesicle Docking, and Synaptic Protein Distribution in the Hippocampus of BDNF Knockout Mice
     J Neurosci, 19:4972-4983 (1999), doi:10.1523/JNEUROSCI.19-12-04972.1999
109. Pozzo-Miller LD, Pivovarova NB, Connor JA, Reese TS, Andrews SB
     Correlated measurements of free and total intracellular calcium concentration in central nervous system neurons
     Microsc Res Tech, 46:370-379 (1999)
110. Pozzo-Miller LD, Inoue T, Murphy DD
     Estradiol increases spine density and NMDA-dependent Ca²⁺ transients in spines of CA1 pyramidal neurons from hippocampal slices
     J Neurophysiol, 81:1404-1411 (1999)
111. Nelson TJ, Zhao WQ, Yuan S, Favit A, Pozzo-Miller L, Alkon DL
     Calexcitin interaction with neuronal ryanodine receptors
     Biochem J, 341:423-433 (1999)
112. Yoshida M, Sensui N, Inoue T, Morisawa M, Mikoshiba K
     Role of two series of Ca²⁺ oscillations in activation of ascidian eggs
     Dev Biol, 203:122-133 (1998), doi:10.1006/dbio.1998.9037
113. Takei K, Shin RM, Inoue T, Kato K, Mikoshiba K
     Regulation of nerve growth mediated by inositol 1,4,5-trisphosphate receptors in growth cones
     Science, 282:1705-1708 (1998), doi:10.1126/science.282.5394.1705
114. Gottschalk W, Pozzo-Miller LD, Figurov A, Lu B
     Presynaptic modulation of synaptic transmission and plasticity by brain-derived neurotrophic factor in the developing hippocampus
     J Neurosci, 18:6830-6839 (1998)
115. Inoue T, Kato K, Kohda K, Mikoshiba K
     Type 1 inositol 1,4,5-trisphosphate receptor is required for induction of long-term depression in cerebellar Purkinje neurons
     J Neurosci, 18:5366-5373 (1998)