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<DIV>Hi Seth,</DIV>
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<DIV>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.</DIV>
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<DIV>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.</DIV>
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<DIV>Jon</DIV>
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<DIV><FONT color=red>> Jon,<BR>><BR>> Thanks for your input. For now I am trying to implement multichannel<BR>> acquisition with the approach that the OpenSPIM plugin takes. From what I’ve<BR>> gathered the approach is not through the MDA but through direct manipulation<BR>> of device properties-historically because of support for the theta axis?<BR>> Disclaimer: I’m not an expert of either. In any event, one of the goals that<BR>> has been discussed on the list is getting the OpenSPIM plugin more in-step<BR>> with ongoing releases of micromanager and perhaps use of MDA might be an<BR>> avenue to explore. But, again this is beyond my experience with the plugin<BR>> thus far(and its design) and better left to a discussion withJohannes.<BR>><BR>
> Since last week, I am able to capture with specific filterwheel and DAC<BR>> settings with the OpenSPIM plugin. The gui I’ve implemented thus far is<BR>> simple and built around the SteppedSlider class Johannes included with the<BR>> OpenSPIM plugin-I’ll take a look at your suggestions for inspiration. There<BR>> are some outstanding things (of course) including, getting micromanager to<BR>> use blanking of the DACs as a shutter-not difficult, but critical, z<BR>> bidirectionality and some image handling details(dealing with the multiple<BR>> channels correctly, which you mention).<BR>><BR>> Once the dust settles I figure out how to push some of this back to<BR>> micromanager, especially the DAC controller(hardware and software) which can<BR>
> be implemented for around $100 (custom shield, Arduino and the open<BR>> micromanager device adapter I’ve modified). Significantly cheaper than any<BR>> of the other options out there. In any event… I’ve rambled a bit.<BR>><BR>> Thanks again for your input!<BR>><BR>> Cheers,<BR>><BR>> Seth<BR>><BR>> From: Jon Daniels <A href="mailto:jon@asiimaging.com"><FONT color=#0000ff>[mailto:jon@asiimaging.com]</FONT></A><BR>> Sent: Wednesday, February 25, 2015 6:36 PM<BR>> To: Winfree, Seth; Johannes Schindelin <A href="mailto:johannes.schindelin@gmx.de"><FONT color=#0000ff>(johannes.schindelin@gmx.de)</FONT></A><BR>> Cc: <A href="mailto:openspim@openspim.org"><FONT color=#0000ff>openspim@openspim.org</FONT></A><BR>
> Subject: re: [OpenSPIM] MultiChannel Acquisition Implementation<BR>><BR>> Hi Seth,<BR>><BR>> I'm no expert in the OpenSPIM code, but I am very familiar with the diSPIM<BR>> plugin in Micro-Manager which does something very similar.<BR>><BR>> If I understand the question correctly, you want to know how to tell<BR>> Micro-Manager which images are from which channels so they will get saved<BR>> correctly in a multi-dimensional dataset. Make sure you add the metadata tag<BR>> "ChannelIndex" to the TaggedImage you are presumably getting from the<BR>> camera's circular buffer and then passing along to the Micro-Manager<BR>> internals. You'll also want to call setChannelName() so that the index is<BR>> linked to a meaningful name. See code at<BR>
> <A href="https://valelab.ucsf.edu/trac/micromanager/browser/plugins/ASIdiSPIM/src/org"><FONT color=#0000ff>https://valelab.ucsf.edu/trac/micromanager/browser/plugins/ASIdiSPIM/src/org</FONT></A><BR>> /micromanager/asidispim/AcquisitionPanel.java, look at<BR>> runAcquisitionPrivate() (line 1506) which sets up the acquisition and then<BR>> calls addImageToAcquisition() (line 2210) which adds the correct metadata<BR>> and inserts the images into the ImageCache queue. See also<BR>> <A href="https://micro-manager.org/wiki/Multi-Dimensional_Acquisition_Programming"><FONT color=#0000ff>https://micro-manager.org/wiki/Multi-Dimensional_Acquisition_Programming.</FONT></A><BR>><BR>> If you are interested in the GUI aspects, see Micro-Manager's MDA window or<BR>> the diSPIM plugin's simplified channel selection table.<BR>
><BR>> Good luck!<BR>><BR>> Jon<BR>><BR>> > Johannes and list,<BR>> ><BR>> > I’ve made pretty good progress on the hardware implementation of multiple<BR>> > channels for our L-SPIM. On the software side I’ve adapted drivers and<BR>> > firmware to control my homebuilt DAC (6ch for now) and NEOS-AOTF setup in<BR>> > micromanager and pulled everything into the SPIMAcquisition plugin with the<BR>> > Device abstraction, a new DAC class and DAC voltage GUI. Eventually there<BR>> > will be a wattage calibration. I also have a Sutter 10-2 implemented inthe<BR>> > SPIMAcquisition plugin via Device and a FilterWheel class. Right now these<BR>> > new devices can be accessed and controlled through SPIMsetup. I do need to<BR>
> > push all these changes to a new branch… getting there.<BR>> ><BR>> > I’m now thinking through the acquisition side of things and before I get to<BR>> > far down a particular path I wanted to see if there were any strong<BR>> opinions<BR>> > about the implementation of multiple channels. I believe I understand how<BR>> > you’ve implemented acquisition and haven’t found a simple way to add the<BR>> > extra dimension of channels (DAC and filter wheel). This could be because<BR>> > I’m missing something in the implementation though.<BR>> ><BR>> > Thanks in advance for your thoughts!<BR>> ><BR>> > Seth<BR>> ><BR>> > Seth Winfree<BR>
> > Indiana Center for Biological Microscopy<BR>> > Indiana University Medical Center<BR>> > 950 West Walnut St, R2-202<BR>> > Indianapolis, IN 46202-5116<BR>> ><BR>> > _______________________________________________<BR>> > OpenSPIM mailing list<BR>> > <A href="mailto:OpenSPIM@openspim.org"><FONT color=#0000ff>OpenSPIM@openspim.org</FONT></A><BR>> > <A href="http://openspim.org/mailman/listinfo/openspim"><FONT color=#0000ff>http://openspim.org/mailman/listinfo/openspim</FONT></A><BR>><BR>> Jon Daniels<BR>> Applied Scientific Instrumentation<BR>> 29391 West Enid Rd, Eugene, OR 97402<BR>> Phone: (541) 461-8181 x118<BR>> US & Canada: (800) 706-2284<BR>> Fax: (541) 461-4018<BR>></FONT><BR> </DIV>
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<P><FONT size=2>Jon Daniels</FONT><FONT size=2><BR><EM><A href="http://www.ASIimaging.com">Applied Scientific Instrumentation</A></EM><BR></FONT><FONT size=1><EM>29391 West Enid Rd, Eugene, OR 97402</EM><BR><EM>Phone: (541) 461-8181</EM> x118<BR><EM>US & Canada: (800) 706-2284</EM><BR><EM>Fax: (541) 461-4018</EM></FONT></P></TH></TR></TBODY></TABLE></DIV></DIV></FONT></BODY></HTML>