Synchronization problem

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Synchronization problem

Kate Luby-Phelps
Hi Nico,

I have been pretty successful so far using 1.3.43 for Mac to control a Zeiss Axioplan motorized scope with a Hamamatsu Orca camera. I am using the Zeiss CAN bus adapters to control the fluorescence filter turret, Z drive and fluorescence shutter through a Keyspan serial adapter. However, When I set up my multi-dimensional acquisition there is a problem synchronizing the camera with the fluorescence shutter. If I have the shutter open (no autoshutter) and then start the acquisition, the exposure time for DAPI is 30 msec. But if I use autoshutter, the camera apparently snaps the picture before the fluorescence shutter is open. I have to change the exposure time to 180 msec to get the whole field. Intermediate exposures give me part of the field starting on the right and moving progressively to the left as I increase the exposure setting. I think the internal fluorescence shutter in this microscope is actually a TTL device and doesn't tell the camera when it is fully open. Is there some way to build in a delay before the camera starts exposing? Or do I just not have things configured properly? I have told the program to synchronize with the Fluorescence Shutter and I have tried many different ways of defining the channels including specifying the shutter state. If I specify the shutter state to be open for each channel definition then everything works but the shutter is open at the end of the sequence. If better synchronization is not possible, I can do it that way but I then need some way to tell it to close the shutter at the end of the acquisition.


Thanks!

******************
I have cut and pasted my config file below:

# Generated by Configurator on Mon Dec 28 14:46:43 CST 2009

# Reset
Property,Core,Initialize,0

# Devices
Device,/dev/tty.USA28X2b2P1.1,SerialManager,/dev/tty.USA28X2b2P1.1
Device,Hamamatsu_DCAM,Hamamatsu,Hamamatsu_DCAM
Device,ZeissScope,ZeissCAN,ZeissScope
Device,ZeissReflectorTurret,ZeissCAN,ZeissReflectorTurret
Device,Focus,ZeissCAN,Focus
Device,Fluorescence Shutter,ZeissCAN,ZeissShutterMFFirmware

# Pre-init settings for devices
Property,Hamamatsu_DCAM,Slot,0
Property,ZeissScope,Port,/dev/tty.USA28X2b2P1.1
Property,Fluorescence Shutter,ZeissShutterNr,1

# Pre-init settings for COM ports
Property,/dev/tty.USA28X2b2P1.1,AnswerTimeout,2000.00
Property,/dev/tty.USA28X2b2P1.1,BaudRate,9600
Property,/dev/tty.USA28X2b2P1.1,DataBits,8
Property,/dev/tty.USA28X2b2P1.1,DelayBetweenCharsMs,0.0000
Property,/dev/tty.USA28X2b2P1.1,Handshaking,Off
Property,/dev/tty.USA28X2b2P1.1,StopBits,1

# Initialize
Property,Core,Initialize,1

# Delays

# Roles
Property,Core,Camera,Hamamatsu_DCAM
Property,Core,Shutter,Fluorescence Shutter
Property,Core,Focus,Focus
Property,Core,AutoShutter,0

# Camera-synchronized devices
ImageSynchro,ZeissScope
ImageSynchro,ZeissReflectorTurret
ImageSynchro,Fluorescence Shutter
ImageSynchro,Focus

# Labels
# ZeissReflectorTurret
Label,ZeissReflectorTurret,4,Cy5
Label,ZeissReflectorTurret,3,Rhod/TxR
Label,ZeissReflectorTurret,2,FITC/GFP
Label,ZeissReflectorTurret,1,DAPI
Label,ZeissReflectorTurret,0,DIC

# Configuration presets
# Group: Channels
# Preset: FITC_GFP
ConfigGroup,Channels,FITC_GFP,ZeissReflectorTurret,Label,FITC/GFP
ConfigGroup,Channels,FITC_GFP,ZeissReflectorTurret,State,2
ConfigGroup,Channels,FITC_GFP,Fluorescence Shutter,State,0

# Preset: DIC
ConfigGroup,Channels,DIC,ZeissReflectorTurret,Label,DIC
ConfigGroup,Channels,DIC,ZeissReflectorTurret,State,0
ConfigGroup,Channels,DIC,Fluorescence Shutter,State,0

# Preset: Rhod_TxR
ConfigGroup,Channels,Rhod_TxR,ZeissReflectorTurret,Label,Rhod/TxR
ConfigGroup,Channels,Rhod_TxR,ZeissReflectorTurret,State,3
ConfigGroup,Channels,Rhod_TxR,Fluorescence Shutter,State,0

# Preset: DAPI
ConfigGroup,Channels,DAPI,ZeissReflectorTurret,Label,DAPI
ConfigGroup,Channels,DAPI,ZeissReflectorTurret,State,1
ConfigGroup,Channels,DAPI,Fluorescence Shutter,State,0

# Preset: Cy5
ConfigGroup,Channels,Cy5,ZeissReflectorTurret,Label,Cy5
ConfigGroup,Channels,Cy5,ZeissReflectorTurret,State,4
ConfigGroup,Channels,Cy5,Fluorescence Shutter,State,0


# Group: Channel

# Group: System
# Preset: Startup


# Group: Focus
# Preset: Up
ConfigGroup,Focus,Up,Focus,Position,274.9750

# Preset: Load Position
ConfigGroup,Focus,Load Position,Focus,Position,-4999.9750


# Group: Camera Gain
# Preset: NewPreset
ConfigGroup,Camera Gain,NewPreset,Hamamatsu_DCAM,Gain,53



# PixelSize settings


Kate Luby-Phelps, Ph.D.

Director, Live Cell Imaging Core Facility

Professor, Dept. of Cell Biology

UT Southwestern Medical Center

5323 Harry Hines Blvd. 

Room K2.220

Dallas, TX 75390-9039


T: 214-648-0429

F: 214-648-8694

Reply to: [hidden email]

Website: http://www4.utsouthwestern.edu/LiveCellImagingFacility/home.html





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Re: Synchronization problem

Arthur D. Edelstein
Hi Kate,

Nico is on vacation -- I hope I can substitute. Please have a look at
Step 6 in the Hardware Configuration Wizard (under the Tools menu),
and try entering a Delay in ms for the fluorescence shutter. The
instructions at the bottom of the window in Step 6 may be of help.

Hope this works for you. Please let me know if it doesn't.

Best regards,
Arthur



On Mon, Dec 28, 2009 at 3:36 PM, Kate Luby-Phelps
<[hidden email]> wrote:

> Hi Nico,
> I have been pretty successful so far using 1.3.43 for Mac to control a Zeiss
> Axioplan motorized scope with a Hamamatsu Orca camera. I am using the Zeiss
> CAN bus adapters to control the fluorescence filter turret, Z drive and
> fluorescence shutter through a Keyspan serial adapter. However, When I set
> up my multi-dimensional acquisition there is a problem synchronizing the
> camera with the fluorescence shutter. If I have the shutter open (no
> autoshutter) and then start the acquisition, the exposure time for DAPI is
> 30 msec. But if I use autoshutter, the camera apparently snaps the picture
> before the fluorescence shutter is open. I have to change the exposure time
> to 180 msec to get the whole field. Intermediate exposures give me part of
> the field starting on the right and moving progressively to the left as I
> increase the exposure setting. I think the internal fluorescence shutter in
> this microscope is actually a TTL device and doesn't tell the camera when it
> is fully open. Is there some way to build in a delay before the camera
> starts exposing? Or do I just not have things configured properly? I have
> told the program to synchronize with the Fluorescence Shutter and I have
> tried many different ways of defining the channels including specifying the
> shutter state. If I specify the shutter state to be open for each channel
> definition then everything works but the shutter is open at the end of the
> sequence. If better synchronization is not possible, I can do it that way
> but I then need some way to tell it to close the shutter at the end of the
> acquisition.
>
> Thanks!
> ******************
> I have cut and pasted my config file below:
> # Generated by Configurator on Mon Dec 28 14:46:43 CST 2009
> # Reset
> Property,Core,Initialize,0
> # Devices
> Device,/dev/tty.USA28X2b2P1.1,SerialManager,/dev/tty.USA28X2b2P1.1
> Device,Hamamatsu_DCAM,Hamamatsu,Hamamatsu_DCAM
> Device,ZeissScope,ZeissCAN,ZeissScope
> Device,ZeissReflectorTurret,ZeissCAN,ZeissReflectorTurret
> Device,Focus,ZeissCAN,Focus
> Device,Fluorescence Shutter,ZeissCAN,ZeissShutterMFFirmware
> # Pre-init settings for devices
> Property,Hamamatsu_DCAM,Slot,0
> Property,ZeissScope,Port,/dev/tty.USA28X2b2P1.1
> Property,Fluorescence Shutter,ZeissShutterNr,1
> # Pre-init settings for COM ports
> Property,/dev/tty.USA28X2b2P1.1,AnswerTimeout,2000.00
> Property,/dev/tty.USA28X2b2P1.1,BaudRate,9600
> Property,/dev/tty.USA28X2b2P1.1,DataBits,8
> Property,/dev/tty.USA28X2b2P1.1,DelayBetweenCharsMs,0.0000
> Property,/dev/tty.USA28X2b2P1.1,Handshaking,Off
> Property,/dev/tty.USA28X2b2P1.1,StopBits,1
> # Initialize
> Property,Core,Initialize,1
> # Delays
> # Roles
> Property,Core,Camera,Hamamatsu_DCAM
> Property,Core,Shutter,Fluorescence Shutter
> Property,Core,Focus,Focus
> Property,Core,AutoShutter,0
> # Camera-synchronized devices
> ImageSynchro,ZeissScope
> ImageSynchro,ZeissReflectorTurret
> ImageSynchro,Fluorescence Shutter
> ImageSynchro,Focus
> # Labels
> # ZeissReflectorTurret
> Label,ZeissReflectorTurret,4,Cy5
> Label,ZeissReflectorTurret,3,Rhod/TxR
> Label,ZeissReflectorTurret,2,FITC/GFP
> Label,ZeissReflectorTurret,1,DAPI
> Label,ZeissReflectorTurret,0,DIC
> # Configuration presets
> # Group: Channels
> # Preset: FITC_GFP
> ConfigGroup,Channels,FITC_GFP,ZeissReflectorTurret,Label,FITC/GFP
> ConfigGroup,Channels,FITC_GFP,ZeissReflectorTurret,State,2
> ConfigGroup,Channels,FITC_GFP,Fluorescence Shutter,State,0
> # Preset: DIC
> ConfigGroup,Channels,DIC,ZeissReflectorTurret,Label,DIC
> ConfigGroup,Channels,DIC,ZeissReflectorTurret,State,0
> ConfigGroup,Channels,DIC,Fluorescence Shutter,State,0
> # Preset: Rhod_TxR
> ConfigGroup,Channels,Rhod_TxR,ZeissReflectorTurret,Label,Rhod/TxR
> ConfigGroup,Channels,Rhod_TxR,ZeissReflectorTurret,State,3
> ConfigGroup,Channels,Rhod_TxR,Fluorescence Shutter,State,0
> # Preset: DAPI
> ConfigGroup,Channels,DAPI,ZeissReflectorTurret,Label,DAPI
> ConfigGroup,Channels,DAPI,ZeissReflectorTurret,State,1
> ConfigGroup,Channels,DAPI,Fluorescence Shutter,State,0
> # Preset: Cy5
> ConfigGroup,Channels,Cy5,ZeissReflectorTurret,Label,Cy5
> ConfigGroup,Channels,Cy5,ZeissReflectorTurret,State,4
> ConfigGroup,Channels,Cy5,Fluorescence Shutter,State,0
>
> # Group: Channel
> # Group: System
> # Preset: Startup
>
> # Group: Focus
> # Preset: Up
> ConfigGroup,Focus,Up,Focus,Position,274.9750
> # Preset: Load Position
> ConfigGroup,Focus,Load Position,Focus,Position,-4999.9750
>
> # Group: Camera Gain
> # Preset: NewPreset
> ConfigGroup,Camera Gain,NewPreset,Hamamatsu_DCAM,Gain,53
>
>
> # PixelSize settings
>
> Kate Luby-Phelps, Ph.D.
>
> Director, Live Cell Imaging Core Facility
>
> Professor, Dept. of Cell Biology
>
> UT Southwestern Medical Center
>
> 5323 Harry Hines Blvd.
>
> Room K2.220
>
> Dallas, TX 75390-9039
>
> T: 214-648-0429
>
> F: 214-648-8694
>
> Reply to: [hidden email]
>
> Website: http://www4.utsouthwestern.edu/LiveCellImagingFacility/home.html
>
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>

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