SPIM Multiview Deconvolution Latest Version for PSF Extraction

Hi Fijiers,

I am looking at the source code of the MultiView Registration Application, more specifically on how to extract the PSFs without running the full deconvolution so as to save them and re-use them as needed.

However, I have the Multiview Reconstruction Application 5.0.8 installed.

However on GitHub, this version is not available! Browsing the many many branches there, I cannot seem to find it. Similarily if @StephanPreibisch or someone would have a minute to explain how I can

  1. Load an XML file
  2. Configure the strict minimum needed to extract the psfs from detected beads and display the full PSFs

That way I can save the PSFs without processing the whole dataset first, but the plugin is so large and calls a lot of static classes that make it difficult to see where the important variables are created…

Any help is greatly appreciated

Hi @oburri,

the version is available on GitHub. You need to check the commits on the master branch, and on Nov 14th the commit is called “release version 5.0.8”. That’s corresponding to the current one in Fiji, also called version 5.0.8, here is the link: https://github.com/fiji/SPIM_Registration/commit/ba4e38c098eb60197b7f040e5bed28a275505cd9

The easiest way to find the code snippets important for you is to use the Debug Mode (for example in Eclipse) and run this class: https://github.com/fiji/SPIM_Registration/blob/master/src/main/java/spim/fiji/plugin/Data_Explorer.java which is the MultiViewReconstruction Application.

We are in the process of separating GUI and processing way better than it is now (many of the branches are part of this), but I think it’ll still be two, three months until we are there. Then it’ll be much easier to access the whole pipeline through scripting, each module will work independently, such as the PSF Extraction.

I hope this helps to get you started,

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