Synchronization problem

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Synchronization problem

Kate Luby-Phelps
Thanks Arthur,

It's a good idea BUT the problem is the fluorescence shutter doesn't appear in step 6. In fact the list of devices at step 6 is not populated.

Kate

Kate Luby-Phelps, Ph.D.
Director, Live Cell Imaging Core Facility
Associate Professor
Department of Cell Biology
K2.220
UT Southwestern Medical School
5323 Harry Hines Blvd.
Dallas, TX 75390-9039

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Today's Topics:

   1. Re: Synchronization problem (Arthur D. Edelstein)
   2. newbie question (E Chalaron)
   3. Re: newbie question (Nico Stuurman)
   4. Re: Multi-D bug?? (Jonathan Compton)


----------------------------------------------------------------------

Message: 1
Date: Mon, 28 Dec 2009 23:07:57 -0800
From: "Arthur D. Edelstein" <[hidden email]>
Subject: Re: [micro-manager-general] Synchronization problem
To: Micro-Manager General
        <[hidden email]>
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1

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
>
>
>
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------------------------------

Message: 2
Date: Sat, 02 Jan 2010 17:43:29 +1300
From: E Chalaron <[hidden email]>
Subject: [micro-manager-general] newbie question
To: [hidden email]
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1

Hello all
Just joined the list for micro manager.
I have seen that it is supporting iidc1394 cameras, does it actually
provide an option the format7 mode (external triggering mode)
Thanks a lot
Edouard
Nz



------------------------------

Message: 3
Date: Mon, 4 Jan 2010 10:21:40 -0800
From: Nico Stuurman <[hidden email]>
Subject: Re: [micro-manager-general] newbie question
To: [hidden email], Micro-Manager General
        <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=us-ascii

Hi Edouard,

> Just joined the list for micro manager.
> I have seen that it is supporting iidc1394 cameras, does it actually
> provide an option the format7 mode (external triggering mode)

Format7 cameras are supported.  However, there are no provisions for changing trigger modes in the current dc1394 implementation.  Should not be too hard to add if you have such a camera and can do some coding;)

Best,

Nico


------------------------------

Message: 4
Date: Mon, 4 Jan 2010 14:37:36 -0800
From: Jonathan Compton <[hidden email]>
Subject: Re: [micro-manager-general] Multi-D bug??
To: [hidden email]
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

Here is the information you requested. I wasn't sure if I send it to the
forum or you as I didnt know what attaching would do.


Here is what I do.

I have 5 positions saved on the XY list, and I want to do a relative z-stack
at say +1 to +4 um.

I start the aquisition and the first position works fine, then the following
positions have the error. They go to the preset Z for the initial frame it
seems then the following frames jump to either the Z of the first position
or the actual z-stack values, ie 1-4um or whatever the preset is for the
first position plus the stack numbers.

I hope this helps.

On Wed, Dec 9, 2009 at 11:17 PM, Jonathan Compton <
[hidden email]> wrote:

> Hello,
>
> I am trying to take a z-stack at multiple locations using the xy list. I
> select relative z and acquire, and it acts as if I chose absolute z by using
> the predefined range as the actual Z positions. I then un-check the use xy
> list button at a location and then it works correctly using the relative z
> range. Is this a bug or what?
>
> --
> Jon
>
>


End of micro-manager-general Digest, Vol 38, Issue 1
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Re: Synchronization problem

Nico Stuurman-4
Hi Kate,

> It's a good idea BUT the problem is the fluorescence shutter doesn't  
> appear in step 6. In fact the list of devices at step 6 is not  
> populated.

Could you email me (off-list) a Corelog.txt file (go to the 'Tools'  
menu in Micro-Manager and select 'Options...'. Click the 'Clear log  
file' button and make sure that the 'Debug log enabled' checkbox is  
checked. Now restart Micro-Manager, repeat the steps that cause the  
error and find the file 'CoreLog.txt' in your Micro-Manager  
directory)?  Our code is interrogating the microscope to ask whether  
the shutter is still moving.  Either the microscope is lying, or (more  
likely since we have never worked with a Zeiss MF Firmware shutter)  
there is something going wrong in the communication between Micro-
manager and the Zeiss microscope.

Best,

Nico



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