[OpenSPIM] MultiChannel Acquisition Implementation

Wed Mar 4 14:32:35 CST 2015

Jon,

Right, you’re not using the MDA in the diSPIM plugin.  I am confusing the parts of MM, MDA vs what is accessible on the main window via the ScriptInterface-I have to put MDA out of my head.  You are using components that the MDA uses but not 'using' the MDA.   I do like the use of the ScriptInterface to implement multiple channels.  Was this to simplify the users experience or to compartmentalize the microscope state using the existing classes?  In any event, I can see the advantage of this approach, why not use the MM acquisition/configuration states.  Then I could take advantage of their functionality.

I’ll think on it.

Thanks again for your input it has been very helpful.

Seth

Winfree, Seth
winfrees at iupui.edu<mailto:winfrees at iupui.edu>

Indiana Center for Biological Microscopy
Indiana University Medical Center
950 W Walnut St, R2-202
Indianapolis, IN 46202-5116

On Mar 4, 2015, at 1:28 PM, Jon Daniels <jon at asiimaging.com<mailto:jon at asiimaging.com>> wrote:

Hi Seth,

To clarify, the diSPIM plugin does not use the MDA either.  Instead it provides a separate GUI for performing acquisitions and Java code to handle the low-level details.

I know that in version 2.0 (still pre-beta I think) the Micro-Manager developers are trying to make it easier to "design your own acquisition", which should simplify things for people like doing acquisitions that don't fit into the MDA paradigm.

Jon

>  Jon,
>
>  Thanks for your input. For now I am trying to implement multichannel
>  acquisition with the approach that the OpenSPIM plugin takes. From what I’ve
>  gathered the approach is not through the MDA but through direct manipulation
>  of device properties-historically because of support for the theta axis?
>  Disclaimer: I’m not an expert of either. In any event, one of the goals that
>  has been discussed on the list is getting the OpenSPIM plugin more in-step
>  with ongoing releases of micromanager and perhaps use of MDA might be an
>  avenue to explore. But, again this is beyond my experience with the plugin
>  thus far(and its design) and better left to a discussion withJohannes.
>
>  Since last week, I am able to capture with specific filterwheel and DAC
>  settings with the OpenSPIM plugin. The gui I’ve implemented thus far is
>  simple and built around the SteppedSlider class Johannes included with the
>  OpenSPIM plugin-I’ll take a look at your suggestions for inspiration. There
>  are some outstanding things (of course) including, getting micromanager to
>  use blanking of the DACs as a shutter-not difficult, but critical, z
>  bidirectionality and some image handling details(dealing with the multiple
>  channels correctly, which you mention).
>
>  Once the dust settles I figure out how to push some of this back to
>  micromanager, especially the DAC controller(hardware and software) which can
>  be implemented for around $100 (custom shield, Arduino and the open
>  micromanager device adapter I’ve modified). Significantly cheaper than any
>  of the other options out there. In any event… I’ve rambled a bit.
>
>  Thanks again for your input!
>
>  Cheers,
>
>  Seth
>
>  From: Jon Daniels [mailto:jon at asiimaging.com]<mailto:jon at asiimaging.com>
>  Sent: Wednesday, February 25, 2015 6:36 PM
>  To: Winfree, Seth; Johannes Schindelin (johannes.schindelin at gmx.de)<mailto:johannes.schindelin at gmx.de>
>  Cc: openspim at openspim.org<mailto:openspim at openspim.org>
>  Subject: re: [OpenSPIM] MultiChannel Acquisition Implementation
>
>  Hi Seth,
>
>  I'm no expert in the OpenSPIM code, but I am very familiar with the diSPIM
>  plugin in Micro-Manager which does something very similar.
>
>  If I understand the question correctly, you want to know how to tell
>  Micro-Manager which images are from which channels so they will get saved
>  correctly in a multi-dimensional dataset. Make sure you add the metadata tag
>  "ChannelIndex" to the TaggedImage you are presumably getting from the
>  camera's circular buffer and then passing along to the Micro-Manager
>  internals. You'll also want to call setChannelName() so that the index is
>  linked to a meaningful name. See code at
>  https://valelab.ucsf.edu/trac/micromanager/browser/plugins/ASIdiSPIM/src/org
>  /micromanager/asidispim/AcquisitionPanel.java, look at
>  runAcquisitionPrivate() (line 1506) which sets up the acquisition and then
>  calls addImageToAcquisition() (line 2210) which adds the correct metadata
>  and inserts the images into the ImageCache queue. See also
>  https://micro-manager.org/wiki/Multi-Dimensional_Acquisition_Programming.<https://micro-manager.org/wiki/Multi-Dimensional_Acquisition_Programming>
>
>  If you are interested in the GUI aspects, see Micro-Manager's MDA window or
>  the diSPIM plugin's simplified channel selection table.
>
>  Good luck!
>
>  Jon
>
>  > Johannes and list,
>  >
>  > I’ve made pretty good progress on the hardware implementation of multiple
>  > channels for our L-SPIM. On the software side I’ve adapted drivers and
>  > firmware to control my homebuilt DAC (6ch for now) and NEOS-AOTF setup in
>  > micromanager and pulled everything into the SPIMAcquisition plugin with the
>  > Device abstraction, a new DAC class and DAC voltage GUI. Eventually there
>  > will be a wattage calibration. I also have a Sutter 10-2 implemented inthe
>  > SPIMAcquisition plugin via Device and a FilterWheel class. Right now these
>  > new devices can be accessed and controlled through SPIMsetup. I do need to
>  > push all these changes to a new branch… getting there.
>  >
>  > I’m now thinking through the acquisition side of things and before I get to
>  > far down a particular path I wanted to see if there were any strong
>  opinions
>  > about the implementation of multiple channels. I believe I understand how
>  > you’ve implemented acquisition and haven’t found a simple way to add the
>  > extra dimension of channels (DAC and filter wheel). This could be because
>  > I’m missing something in the implementation though.
>  >
>  > Thanks in advance for your thoughts!
>  >
>  > Seth
>  >
>  > Seth Winfree
>  > Indiana Center for Biological Microscopy
>  > Indiana University Medical Center
>  > 950 West Walnut St, R2-202
>  > Indianapolis, IN 46202-5116
>  >
>  > _______________________________________________
>  > OpenSPIM mailing list
>  > OpenSPIM at openspim.org<mailto:OpenSPIM at openspim.org>
>  > http://openspim.org/mailman/listinfo/openspim
>
>  Jon Daniels
>  Applied Scientific Instrumentation
>  29391 West Enid Rd, Eugene, OR 97402
>  Phone: (541) 461-8181 x118
>  US & Canada: (800) 706-2284
>  Fax: (541) 461-4018
>

[ASI]
Jon Daniels
Applied Scientific Instrumentation<http://www.asiimaging.com/>
29391 West Enid Rd, Eugene, OR 97402
Phone: (541) 461-8181 x118
US & Canada: (800) 706-2284
Fax: (541) 461-4018

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