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software:micro-manager [2023/08/16 21:03]
Jon Daniels [Micro-manager diSPIM Plugin] 		software:micro-manager [2024/05/21 23:52] (current)
Jon Daniels [Runnables in the plugin]
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 Currently the diSPIM plugin is supported in 1.4.x only.  In 2023 there have been efforts to create a new plugin in Micro-Manager 2.0 called [[https://github.com/micro-manager/LightSheetManager|LightSheetManager]] that will operate the diSPIM as well as other types of light sheet microscopes.  Contributions to the effort of making this new plugin are appreciated.  As of August 2023 this is in alpha testing by the first few bleeding edge adopters, and we expect that by end of 2023 it will be ready for more adopters and a full replacement in 2024. Currently the diSPIM plugin is supported in 1.4.x only.  In 2023 there have been efforts to create a new plugin in Micro-Manager 2.0 called [[https://github.com/micro-manager/LightSheetManager|LightSheetManager]] that will operate the diSPIM as well as other types of light sheet microscopes.  Contributions to the effort of making this new plugin are appreciated.  As of August 2023 this is in alpha testing by the first few bleeding edge adopters, and we expect that by end of 2023 it will be ready for more adopters and a full replacement in 2024.
  
-You can download the nightly builds of Micro-manager 1.4 for Windows [[http://valelab4.ucsf.edu/~MM/nightlyBuilds/1.4/Windows/|here]]; the date is encoded in the file name and the latest date is at the top of the page.  Make sure to get the appropriate 32bit or 64bit depending on your computer.+You can download the nightly builds of Micro-manager 1.4 for Windows [[https://download.micro-manager.org/nightly/1.4/Windows/|here]]; the date is encoded in the file name and the latest date is at the top of the page.  Make sure to get the appropriate 32bit or 64bit depending on your computer.
  
  
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 diSPIM.attachRunnable(taskStartTimepoint, RunnableType.TIMEPOINT_START); diSPIM.attachRunnable(taskStartTimepoint, RunnableType.TIMEPOINT_START);
 diSPIM.attachRunnable(taskEndTimepoint, RunnableType.TIMEPOINT_END); diSPIM.attachRunnable(taskEndTimepoint, RunnableType.TIMEPOINT_END);
 +
 +</code>
 +
 +
 +Here is another example that runs autofocus periodically, in this case every 13 positions.
 +
 +<code>
 +
 +// runs autofocus once on the first position and periodically afterwards based on period set in script (currently every 13th position)
 +// script assumes that CRISP is already set up and is the default focus device
 +// run this script after launching the plugin and before beginning the acquisition
 +
 +// required imports
 +import org.micromanager.asidispim.api.*;
 + 
 +// get a reference to the plugin; use this to call the plugins API methods
 +ASIdiSPIMInterface diSPIM = new ASIdiSPIMImplementation();
 +
 +// local variables
 +int runnablePositionCounter;
 +int counterPeriod = 13;
 + 
 +// initialize the counter when the acquisition begins
 +taskStartAcquisition = new Runnable() {
 + public void run() {
 + runnablePositionCounter = 0;
 + }
 +};
 +
 +// at each position see if it's time to run autofocus, plus also increment the counter
 +taskStartPosition = new Runnable() {
 + public void run() {
 + //gui.showError("started position " + runnablePositionCounter);
 + if ((runnablePositionCounter % counterPeriod)<1) {
 + mmc.fullFocus();   // this is supposed to be a blocking call in the device adapter (should wait until focus is achieved)
 + }
 + runnablePositionCounter++;
 + }
 +};
 +
 + 
 +// add the runnables to the diSPIM plugin's acquisition engine
 +diSPIM.clearAllRunnables();
 +diSPIM.attachRunnable(taskStartAcquisition, RunnableType.ACQUISITION_START);
 +diSPIM.attachRunnable(taskStartPosition, RunnableType.POSITION_START);
 +
  
 </code> </code>

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