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Jon,
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<div class="">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. </div>
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<div class="">I’ll think on it. </div>
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<div class="">Thanks again for your input it has been very helpful.</div>
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<div class="">Seth</div>
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<div class="">Winfree, Seth</div>
<div class=""><a href="mailto:winfrees@iupui.edu" class="">winfrees@iupui.edu</a></div>
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<div class="">Indiana Center for Biological Microscopy</div>
<div class="">Indiana University Medical Center</div>
<div class="">950 W Walnut St, R2-202</div>
<div class="">Indianapolis, IN 46202-5116</div>
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<div class="">On Mar 4, 2015, at 1:28 PM, Jon Daniels <<a href="mailto:jon@asiimaging.com" class="">jon@asiimaging.com</a>> wrote:</div>
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<div class="">Hi Seth,</div>
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<div class="">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 class="">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 class="">Jon</div>
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<div class=""><font color="red" class="">> Jon,<br class="">
><br class="">
> Thanks for your input. For now I am trying to implement multichannel<br class="">
> acquisition with the approach that the OpenSPIM plugin takes. From what I’ve<br class="">
> gathered the approach is not through the MDA but through direct manipulation<br class="">
> of device properties-historically because of support for the theta axis?<br class="">
> Disclaimer: I’m not an expert of either. In any event, one of the goals that<br class="">
> has been discussed on the list is getting the OpenSPIM plugin more in-step<br class="">
> with ongoing releases of micromanager and perhaps use of MDA might be an<br class="">
> avenue to explore. But, again this is beyond my experience with the plugin<br class="">
> thus far(and its design) and better left to a discussion withJohannes.<br class="">
><br class="">
> Since last week, I am able to capture with specific filterwheel and DAC<br class="">
> settings with the OpenSPIM plugin. The gui I’ve implemented thus far is<br class="">
> simple and built around the SteppedSlider class Johannes included with the<br class="">
> OpenSPIM plugin-I’ll take a look at your suggestions for inspiration. There<br class="">
> are some outstanding things (of course) including, getting micromanager to<br class="">
> use blanking of the DACs as a shutter-not difficult, but critical, z<br class="">
> bidirectionality and some image handling details(dealing with the multiple<br class="">
> channels correctly, which you mention).<br class="">
><br class="">
> Once the dust settles I figure out how to push some of this back to<br class="">
> micromanager, especially the DAC controller(hardware and software) which can<br class="">
> be implemented for around $100 (custom shield, Arduino and the open<br class="">
> micromanager device adapter I’ve modified). Significantly cheaper than any<br class="">
> of the other options out there. In any event… I’ve rambled a bit.<br class="">
><br class="">
> Thanks again for your input!<br class="">
><br class="">
> Cheers,<br class="">
><br class="">
> Seth<br class="">
><br class="">
> From: Jon Daniels<span class="Apple-converted-space"> </span><a href="mailto:jon@asiimaging.com" class=""><font color="#0000ff" class="">[mailto:jon@asiimaging.com]</font></a><br class="">
> Sent: Wednesday, February 25, 2015 6:36 PM<br class="">
> To: Winfree, Seth; Johannes Schindelin<span class="Apple-converted-space"> </span><a href="mailto:johannes.schindelin@gmx.de" class=""><font color="#0000ff" class="">(johannes.schindelin@gmx.de)</font></a><br class="">
> Cc:<span class="Apple-converted-space"> </span><a href="mailto:openspim@openspim.org" class=""><font color="#0000ff" class="">openspim@openspim.org</font></a><br class="">
> Subject: re: [OpenSPIM] MultiChannel Acquisition Implementation<br class="">
><br class="">
> Hi Seth,<br class="">
><br class="">
> I'm no expert in the OpenSPIM code, but I am very familiar with the diSPIM<br class="">
> plugin in Micro-Manager which does something very similar.<br class="">
><br class="">
> If I understand the question correctly, you want to know how to tell<br class="">
> Micro-Manager which images are from which channels so they will get saved<br class="">
> correctly in a multi-dimensional dataset. Make sure you add the metadata tag<br class="">
> "ChannelIndex" to the TaggedImage you are presumably getting from the<br class="">
> camera's circular buffer and then passing along to the Micro-Manager<br class="">
> internals. You'll also want to call setChannelName() so that the index is<br class="">
> linked to a meaningful name. See code at<br class="">
> <a href="https://valelab.ucsf.edu/trac/micromanager/browser/plugins/ASIdiSPIM/src/org" class=""><font color="#0000ff" class="">https://valelab.ucsf.edu/trac/micromanager/browser/plugins/ASIdiSPIM/src/org</font></a><br class="">
> /micromanager/asidispim/AcquisitionPanel.java, look at<br class="">
> runAcquisitionPrivate() (line 1506) which sets up the acquisition and then<br class="">
> calls addImageToAcquisition() (line 2210) which adds the correct metadata<br class="">
> and inserts the images into the ImageCache queue. See also<br class="">
> <a href="https://micro-manager.org/wiki/Multi-Dimensional_Acquisition_Programming" class=""><font color="#0000ff" class="">https://micro-manager.org/wiki/Multi-Dimensional_Acquisition_Programming.</font></a><br class="">
><br class="">
> If you are interested in the GUI aspects, see Micro-Manager's MDA window or<br class="">
> the diSPIM plugin's simplified channel selection table.<br class="">
><br class="">
> Good luck!<br class="">
><br class="">
> Jon<br class="">
><br class="">
> > Johannes and list,<br class="">
> ><br class="">
> > I’ve made pretty good progress on the hardware implementation of multiple<br class="">
> > channels for our L-SPIM. On the software side I’ve adapted drivers and<br class="">
> > firmware to control my homebuilt DAC (6ch for now) and NEOS-AOTF setup in<br class="">
> > micromanager and pulled everything into the SPIMAcquisition plugin with the<br class="">
> > Device abstraction, a new DAC class and DAC voltage GUI. Eventually there<br class="">
> > will be a wattage calibration. I also have a Sutter 10-2 implemented inthe<br class="">
> > SPIMAcquisition plugin via Device and a FilterWheel class. Right now these<br class="">
> > new devices can be accessed and controlled through SPIMsetup. I do need to<br class="">
> > push all these changes to a new branch… getting there.<br class="">
> ><br class="">
> > I’m now thinking through the acquisition side of things and before I get to<br class="">
> > far down a particular path I wanted to see if there were any strong<br class="">
> opinions<br class="">
> > about the implementation of multiple channels. I believe I understand how<br class="">
> > you’ve implemented acquisition and haven’t found a simple way to add the<br class="">
> > extra dimension of channels (DAC and filter wheel). This could be because<br class="">
> > I’m missing something in the implementation though.<br class="">
> ><br class="">
> > Thanks in advance for your thoughts!<br class="">
> ><br class="">
> > Seth<br class="">
> ><br class="">
> > Seth Winfree<br class="">
> > Indiana Center for Biological Microscopy<br class="">
> > Indiana University Medical Center<br class="">
> > 950 West Walnut St, R2-202<br class="">
> > Indianapolis, IN 46202-5116<br class="">
> ><br class="">
> > _______________________________________________<br class="">
> > OpenSPIM mailing list<br class="">
> ><span class="Apple-converted-space"> </span><a href="mailto:OpenSPIM@openspim.org" class=""><font color="#0000ff" class="">OpenSPIM@openspim.org</font></a><br class="">
> ><span class="Apple-converted-space"> </span><a href="http://openspim.org/mailman/listinfo/openspim" class=""><font color="#0000ff" class="">http://openspim.org/mailman/listinfo/openspim</font></a><br class="">
><br class="">
> Jon Daniels<br class="">
> Applied Scientific Instrumentation<br class="">
> 29391 West Enid Rd, Eugene, OR 97402<br class="">
> Phone: (541) 461-8181 x118<br class="">
> US & Canada: (800) 706-2284<br class="">
> Fax: (541) 461-4018<br class="">
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<div style="margin: 0px auto;" class=""><font size="2" class="">Jon Daniels</font><font size="2" class=""><br class="">
<em class=""><a href="http://www.asiimaging.com/" style="color: rgb(0, 87, 155);" class="">Applied Scientific Instrumentation</a></em><br class="">
</font><font size="1" class=""><em class="">29391 West Enid Rd, Eugene, OR 97402</em><br class="">
<em class="">Phone: (541) 461-8181</em><span class="Apple-converted-space"> </span>x118<br class="">
<em class="">US & Canada: (800) 706-2284</em><br class="">
<em class="">Fax: (541) 461-4018</em></font></div>
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