micro-manager-anounce — Low volume. Announcements (releases, news) only.

[micro-manager-anounce] Split view plugin

[Dibyendu K. S. <sa...@uc...>]

Hi All,

I use the split view plugin for two-color FRET experiment (by Opto
split-iii). However, it only shows the composite view of two channels.

For a better understanding of the experiment, we need separate channels
which show individually side by side in addition to the composite view.

The data for two channel recording is saved as one stack, not as two
channel stack, which is difficult to analyze in postprocessing.

Is anyone has experience of working with the split view plugin or similar
in micromanager? Nikon Element software has a nice feature: one for
composite, one for donor channel and another for acceptor channel show side
by side. A similar view in micromanager would be great.

Your advice or suggestions would be highly appreciated.

Thank you,


Dibyendu






--------
Dibyendu K. Sasmal, PhD
Postdoctoral Scholar
The Institute for Molecular Engineering
The University of Chicago

E-mail: sa...@uc... & dsa...@gm...
https://scholar.google.com/citations?hl=en&user=l5F3JREAAAAJ&view_op=list_works&sortby=pubdate
http://ime.uchicago.edu/huang_group/people/dibyendu_kumar_sasmal/

Re: [micro-manager-anounce] micromanager 1.2 Mac version request

[Alessandro Di M. <a.d...@bh...>]

Hello Pariksheet,
Thanks a lot for the note below. It is much appreciated!
Unfortunately I'm still unable to have uManager working with the camera.
I know the camera works with another software but I would still try using ExCap. Any clue on where to find it? I did follow the link [2] below but I could not find it. However, that link was useful to know what to look for in term of config files. As a matter of facts, I did install uManager 1.3.22 and try to load MMConfig_ham.cfg but it crashed again. 
In Addition, being an OS X 10.4 there are no compatible DCAM drivers. 

What else should I try/do? Is there anybody in the community who can send me the old 1.2 version of uM.

Thanks again for all the help.

Best Regards,
Alex




Alessandro Di Maio Ph.D.
Birmingham Adv. Light Microscopy (BALM) Exp. Officer 
School of Biosciences 
University of Birmingham - Edgbaston, 
Birmingham B15 2TT United Kingdom
ph: +44-121-4142503
email: A.D...@bh...
http://www.birmingham.ac.uk/facilities/balm/index.aspx


-----Original Message-----
From: Pariksheet Nanda [mailto:par...@gm...] 
Sent: 30 May 2015 16:53
To: mic...@li...
Subject: Re: [micro-manager-anounce] micromanager 1.2 Mac version request

On Thu, May 28, 2015 at 3:34 PM, Alessandro Di Maio <a.d...@bh...> wrote:
> I wanted to download Micro-Manager 1.2 Mac version but apparently I do 
> not have access to the page…

1) Continuing from your old thread [1], can you confirm you are able to snap images with your  Hamamatsu Orca C4742-95 camera in some other software?  You mentioned it used to work with OpenLab; does that still work?  If you can't test it in OpenLab for whatever reason, the Micro-Manager wiki page for Hamamatsu also mentions using ExCap [2] to test the camera works.  If the camera doesn't snap an image, one would need to be resolve the camera driver / OS compatibility first before trying to use it with Micro-Manager, and your working with Hamamatsu directly would be most efficient to get access to older driver versions and they would know the nuances of compatibility with your older hardware.

2) As Mark mentioned, there are 2 different downloads for Micro-Manager on OS X 10.4, depending on whether the Mac is a newer Intel or an older PPC model.  Per these instructions, check which type of processor you have:
https://support.apple.com/en-us/HT201580
Those Micro-Manager 1.2 links also give me "403 forbidden" permission errors, e.g. [3].
In the mean time, you might also try the Micro-Manager 1.3 downloads which offer both PPC and Intel versions:
https://micro-manager.org/wiki/Micro-Manager_Version_Archive


> Alex

Pariksheet

[1] http://micro-manager.3463995.n2.nabble.com/uM1-4-15-crashes-when-opening-hardware-config-wizard-on-MacOS-10-4-td7585347.html
[2] https://micro-manager.org/wiki/Hamamatsu
[3] http://valelab.ucsf.edu/~nenad/micro-manager/distribution/Micro-Manager_Mac(PPC)_1.2.39.dmg

------------------------------------------------------------------------------
_______________________________________________
micro-manager-anounce mailing list
mic...@li...
https://lists.sourceforge.net/lists/listinfo/micro-manager-anounce

Re: [micro-manager-anounce] micromanager 1.2 Mac version request

[Pariksheet N. <par...@gm...>]

On Thu, May 28, 2015 at 3:34 PM, Alessandro Di Maio <a.d...@bh...> wrote:
> I wanted to download Micro-Manager 1.2 Mac version but apparently I do
> not have access to the page…

1) Continuing from your old thread [1], can you confirm you are able
to snap images with your  Hamamatsu Orca C4742-95 camera in some other
software?  You mentioned it used to work with OpenLab; does that still
work?  If you can't test it in OpenLab for whatever reason, the
Micro-Manager wiki page for Hamamatsu also mentions using ExCap [2] to
test the camera works.  If the camera doesn't snap an image, one would
need to be resolve the camera driver / OS compatibility first before
trying to use it with Micro-Manager, and your working with Hamamatsu
directly would be most efficient to get access to older driver
versions and they would know the nuances of compatibility with your
older hardware.

2) As Mark mentioned, there are 2 different downloads for
Micro-Manager on OS X 10.4, depending on whether the Mac is a newer
Intel or an older PPC model.  Per these instructions, check which type
of processor you have:
https://support.apple.com/en-us/HT201580
Those Micro-Manager 1.2 links also give me "403 forbidden" permission
errors, e.g. [3].
In the mean time, you might also try the Micro-Manager 1.3 downloads
which offer both PPC and Intel versions:
https://micro-manager.org/wiki/Micro-Manager_Version_Archive


> Alex

Pariksheet

[1] http://micro-manager.3463995.n2.nabble.com/uM1-4-15-crashes-when-opening-hardware-config-wizard-on-MacOS-10-4-td7585347.html
[2] https://micro-manager.org/wiki/Hamamatsu
[3] http://valelab.ucsf.edu/~nenad/micro-manager/distribution/Micro-Manager_Mac(PPC)_1.2.39.dmg

[micro-manager-anounce] micromanager 1.2 Mac version request

[Alessandro Di M. <a.d...@bh...>]

Hi,

Following up the answer to my thread regarding the issue of uM1.4.15 crashing when opening hardware config wizard (thanks a lot Mark!!!), I wanted to download Micro-Manager 1.2 Mac version but apparently I do not have access to the page...
Any clues? I can't change to winOS as the PCI card for the Camera is for Mac only so, I have to work on the software side!
Thanks a lot again for the help!

Best,
Alex

[micro-manager-anounce] new MM 1.4.20 in Zeiss AxioPlan 2: the option to choose ZeissShutterMFFirmware is not present

[Fang Z. <fan...@he...>]

Hi, all:

 

I am using the newest MM version 1.4.20 to control AxioPlan 2. All
components are recognized and controlled properly excepting the shutter. The
check lists do not have an entry for ZeissShutterMFFirmware. The only choice
seems to be ZeissShutter. If I checked this, MM complained cannot
communicate with it, then I have to remove it to get through. As a result,
the FL-shutter is on microscope cannot be controlled in MM.
Instead, MM automatically picked up ZeissHalogenLamp state as its shutter
control. The button Open/close truthfully control Halogen lamp.
 
On another Zeiss AxioPlan 2+ imaging, the shutter is controlled properly by
this version, the configuration went smoothly without complaint.
 
I tried three times of re-configuration, the results were the same, no
ZeissShutterMFFirmware came up for choose. Did I miss something obvious?
 
Any suggestion is highly appreciated!

 

Best,

 

Fang

 

[micro-manager-anounce] intermittent communication to CSUX1A1H

[Rick Heil-C. <ric...@gm...>]

Hi All,

I am having only intermittent communication with the CSUX1A1H that I am
working on.  I am not sure if it is the CSUX adapter, the cyberserial
PCI-serial card, or an incompatibility of putting this on a computer
configured to run a red shirt system.  The issues (*italicized and
underlined*), and the description of the system are below.  Any suggestions
to get past these issues would be greatly appreciated.

*Errors during set-up.*

Step 3 of 9: add or remove devices


NAME  ADAPTER/LIBRARY   DESCRIPTION
core  MMcore/default   core controller
CSU Main CSUX-HUB/CSUX   CSUX Hub (Needed for CSUX)
CSU FilterWheel CSUX-Filter Wheel/CSUX  Filter Wheel
CSU Dichroic CSUX-Dichroic Mirror/CSUX Dichroic Mirror
CSU Shutter CSUX-Shutter/CSUX  Shutter
CSU DriveSpeed CSUX-DriveSpeed/CSUX  DriveSpeed
Dummy Camera DCam/DemoCamera   Demo Camera
Dummy Fast Cam DRGBCam/DemoRGBCamer  Demo Streaming Camera

Step 4 of 9 edit pre-initialization settings

Device  Property Value
CSU Main Port  Com8
CSU FilterWheel WheelNumber 1



***NOTE: INTERMITTANT MESSAGE:  "Message: Error code: 22  COM8, Error code
101(65 hex)".  Can not get past, but if hit back and then next you can move
to step 5 of 9***

Step 5 of 9: Select default devices and choose auto-shutter setting.

Default Camera "Dummy Fast Cam"
Default shutter "CSU Shutter"
Defai;t focus stage blank
Auto-Shutter box "checked"

Step 6 of 9:  Set delays for devices without synchronization capabilities
Name  Adapter  Delay [ms]
CSU Shutter CSUX-Shutter 1.0

Step 7 of 9:  Select devices to synchronize wtih image aquisition
CSU Main
CSU Dichroic
CSU FilterWheel
CSU Shutter
CSU DriveSpeed

step 8 of 9: Define Labels for state devices

State Devices  State Label
CSU FilterWheel  0 482
   1 525
   2 583
   3 none
   4 none
   5 none

CSU Dichroic  0 488
   1 457/514
   2 none

CSU DriveSpeed nothing to select

Step 9 of 9: test configuration, save and exit

config file
C:\Program Files\Micro-Manager-1.3\XXXXXX.cfg
Save and test overwrites previous config of same name and "Success!" message
appears

I next go to "property Browser"

When I select different Filterwheel lable values, the value changes and the
corresponding filterwheel state changes appropriately.  Hardware also moves
appropriately.


*When I select different CSU Dichroic-Label values the values intermittently
do not change.  If it does not change, going between the previous and
attempted position will not cause any change.  However, if I choose teh
other postion of the three the dichroic will move.  The motor sounds as if
it is turning a full rotation rather than a single position when the
movement resumes.  A similar behaviour occurs when changing the value of the
CSU Dichroic State.*

When I change the value associated with the property "CSU Drive Speed-State
with the slider the speed will intermittently change.  More offen the
following message pops up.

*Message:  Exception occurred: Error code: 22
CSU Drive Speed
CSUX-DriveSpeed. Serial command failed.  Is the device connected to the
serial port?. (error code 14)*

Additional message in response to moving slider value for drive speed

*Message:
Exception occurred: Error code: 22
CSU FilterWheel
CSU-Filter Wheel. Invalid state (position) requested.*

If I move it small amounts it is OK.  When I change the Answer time out in
config wiz to 10,000.0000 ms the slider is less sensitive to errors.


In Aquisition window, when I select adjustable speed from presets I get an
error message:

*Message:
Exception occurred: Error code: 22
CSU DriveSpeed
CSUX-DriveSpeed. Error code 10004(2714 hex). (Error code: 10004)
Device error encountered*



*Channel Presets.
Get intermittant movelment between channel presets defined as Filterwheel
label and state, and dichroic wheel and state.  More of an issue with moving
to 488 than to either channel with 457/514 dichroic in place.*

*System listed below*

Computer:

 Provided By Red Shirt with Red Shirt imaging system installed

 Dell Precision PWS380
 Intel(R)
 Pentium(R)D CPU 3.00GHz
 2.99 GHz, 2.0 GB of RAM
 Physical Address Extension

 Microscoft Windows XP
 Professional
 Version 2002
 Service Pack 3

Com Ports:
 SIIG CyberSerial 4S 16550 four port serial I/O card
 ports assigned 8, 9, 10, 11
 driver SIIG 6.5.1.5
 driver date:  6/22/2007

Hardware attempting to control with micromanager (will add parrallel port
TTLs of AOTF later, will use dummy camera in MM and stream RedShirt NeuroCCD
in redshirt software while controllilng CSUX1 and AOTF with MM)
 CSUX1A1H via serial: com port 8
  one filter wheel
  motorized dichroic
  shutter
  disk speed

 com port 8 settings in device manager/com ports
  bits per second:   115200
  data bits:    8
  Parity:    none
  stop bits:    1
  flow control:    none

 com port 8 settings in Hardware Configuration Wizard
  Answer Timeout:   6000.0000
  Baud Rate:  115200
  Delay between CharsMs: 0.0000
  Handshaking:  off
  Parity:   none
  StopBits:  1
Thanks,
Rick

[micro-manager-anounce] leica + bugs number format

[Thomas B. <tho...@sn...>]

Hello,

I've successfully succeeded to talk to our leica dmirbe microscope. But  
I do not know how to get the answer :

ret = GetSerialAnswer(port_.c_str(), "\r", answer);
   printf("*****************name: %s",answer);

answer is often null and if not since it includes a \r character, it 
goes at the beginning at the line; how I get the correct values from my 
answer ? and extract any valuable information, kind of substring ?

With my zstage from the microscope I succeeded once to get a focal serie 
,then ,when I tried again it crashed saying com1 closed, do I miss 
something ?

And I have noticed some bugs related to number format, in acquisition  
when you type values greater than 1000 or with . the values is formatted 
using locale setting so in france we get , instead of . , so there is a 
problem when next reading thevalues from the textfields.

Thomas

-- 
/*****************************************************/
     Thomas Boudier, MCU Université Paris 6,
     UMR 7101 / IFR 83. Bat A 328, Campus Jussieu.
     Tel : 01 44 27 3578/2013  Fax : 01 44 27 25 08
/****************************************************/

[micro-manager-anounce] Driver for Zeis axiocam MRm

[<fre...@ep...>]

How can I find the driver for Zeiss axiocam MRm and use with =
micro-manager.
=20
Is it working If I use in the configuration file from micro-manager the =
PVCAM (this is the driver for universal camera) ?
=20
Thank you for your answer.
=20
=20
=20
=20

[micro-manager-anounce] Announcing version 1.0 of Micro-Manager

[Nico S. <ni...@cm...>]

This is to announce the first full release of Micro-Manager 1.0.    
Micro-Manager is an Open Source software package for microscope   
image  acquisition.  Micro-Manager runs as an ImageJ plugin and has   
an easy to use graphical interface. It controls a number of cameras,   
shutters,  filter wheels, stages and other devices, enabling    
acquisition of time-lapses, z-stacks and multi-channel images.

Micro-Manager can be found at http://micro-manager.org.  Executables   
for Windows and Mac OS X are available, as well as the full source   
code which can be build on Windows, Mac OS X and Linux.  We  
encourage  users who wish to stay informed about the latest  
developments and  receive feedback from the user community to  
subscribe to our mailing  list (https:// lists.sourceforge.net/lists/ 
listinfo/micro-manager- general).

Currently, Micro-Manager supports Hamamatsu, PVCAM, Andor and DVC    
cameras, Nikon and Zeiss microscopes, and peripherals from ASI,   
Ludl,  Prior, Sutter, and Vincent (Uniblitz), but anyone can add   
device support by using the Device Developer's Kit.  Also, hardware   
supported by Micro-Manager can be accessed programatically in a   
device-independent way from any Java or C++ program and Matlab.

We welcome your feedback, comments, and bug reports.

Best,

Nenad Amodaj and Nico Stuurman

micro-manager.org
Vale lab
UCSF

[micro-manager-anounce] Micro-Manager 1.0.58 (beta) available

[Nenad A. <ne...@am...>]

All,

Micro-Manager 1.0.58 (beta) is now available on 
http://www.micro-manager.org/downloads.php.

List of changes is this release:

    * Hamamatsu driver updated with additional support for Gamma settings
    * Vincent shutter controller driver changed to support multiple
      models: VMM-D1/T1,D122 and VMM-D3/D4. Controller names changed, so
      this may break your existing configuration. You can use
      Configuration Wizard to update your configuration file. For more
      information on setting up the Vincent controller see Nico's recent
      email quoted below.
    * XYStage API bug fixed: getting the x and y coordinates in Java
      environment. The Java API was slightly modified to allow proper
      update of output values for x and y coordinates.
    * ImageJ now stays open and running after shutting down
      Micro-Manager plugin.
    * Micro-Manager now implicitly executes a startup script. The script
      must reside in the root directory, must be called "MMStartup.bsh"
      and must be written in Beanshell (Java scripting language). The
      script is optional and the program will take no actions if it
      doesn't find the script file. This feature does not require any
      action on your part if you are not interested in using it.

Best regards,
--Nenad


_Instructions for Vincent multiple shutter configurations:_

"To tell Micro-Manager about your shutters, go to the Hardware 
Configuration Wizard (under the Tools menu in Micro-Manager), and add 
the Vincent D3 adapter 3 (or 4) times.  Name them something like Ch1, or 
anything else that makes sense to you.  In the next page, set each of 
these shutters to the same serial port, and assign each shutter to one 
of the three channels.  You could assign the fourth channel to 'All', 
but I don't know how useful it is to switch all channels off and on 
simultaneously.

You will also need to set which shutter to use in your channel 
configuration.  If you already have a group 'Channel' defined you might 
want to delete this first.  Add the group 'Channel' (the name is 
important since it will be used in the Acquisition page).  Make sure 
that you check the box in the 'Use' column for everything that you want 
to be set in your Channel group (filter wheels, dichroics etc..), but 
also for Core-shutter.  Set the Core-shutter to one of your three 
shutters appropriate for the given channel. "