Create a top-to-bottom view on a rendered 3D image (created from stacks of images)?

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• Using Renjin packages inside a R file run by @ScriptManager

  I am trying to use csvread and ggplot inside a R script which is executed with scriptService.run but am getting the following error:

  org.renjin.eval.EvalException: Could not load package org.renjin.cran:csvread; tried org.renjin.cran:csvread, org.renjin.bioconductor:org.renjin.cran:csvread, org.renjin.cran:org.renjin.cran:csvread
  

  The Java code is fairly simple:

  scriptService.run(plotgeneration_file, true);
  

  Inside R I am loading the library as follow:

  library('org.renjin.cran:csvread')
  

  Trying to load it directly with library('csvread') failed similarly.

  I am loading the appropriate dependencies inside the pom.xml:

  <dependencies>
          <dependency>
              <groupId>net.imagej</groupId>
              <artifactId>imagej</artifactId>
          </dependency>
          <dependency>
              <groupId>org.renjin.cran</groupId>
              <artifactId>ggplot2</artifactId>
              <version>3.2.0-b8</version>
          </dependency>
          <dependency>
              <groupId>org.renjin.cran</groupId>
              <artifactId>csvread</artifactId>
              <version>1.2.1-b1</version>
          </dependency>
      </dependencies>
  
• Using an ImageJ macro/script to set threshold and save the settings

  I will be analyzing pictures where I want to threshold out interesting objects and then use the particle plugin to count them etc. This will be done one a lot of pictures and I want to use a few different automatic threshold methods and a manual one to make sure that the findings are not dependent on a specific threshold setting.

  The automatic ones are easy to do but for the manual one I want to save the settings for each file that I do to make sure that there is not a big difference between groups.

  The question is: Is there a way to create a macro/script that opens the threshold windows, lets you set the values for the threshold and store them. And then continue the script. Any help that could point me in the right direction to get started would be very appreciated.

  The closes I have gotten is

  run("Threshold..."); 
  
  waitForUser("select threshold, then hit OK"); 
  getThreshold(lower,upper)      
  print("your thresholds are; "+lower, "to "+ upper);  
  

  This does what I want but it requires the user to set the threshold press OK then hit apply. If apply is hit first it adds the mask and all value become 255. Hence, It is very sensitive to pressing buttons in the correct order.

  I tried it also in javascript but then i did not even get to chose anything in the dialog box:

  importClass(Packages.ij.IJ);
  importClass(Packages.ij.plugin.frame.RoiManager);
  importClass(Packages.ij.gui.GenericDialog);
  
  IJ.run("Threshold");
  
• How do I stack 50 PNG images into a MRC image using command line tool?

  As the title suggests, I'm looking for a solution to stack n (n>50) PNG images into a MRC image. I know how to do this using Fiji app (GUI) but have no idea how to do so using command line.

  OS: OS X or Linux

  Any solution using popular framework (e.g. OpenCV) in Python is also welcomed.
• Unknown module(s) in QT: 3dextras

  In .pro file added "QT += 3dextras"

  In Tools->Options->kits added "/usr/lib/x86_64-linux-gnu/qt5/bin/qmake"

  But still getting an error-

  :-1: error: Unknown module(s) in QT: 3dextras
• Why SCNView not working on iphone XS Max?

  I have a scene create programmatically. It's working on everything, then one day, a QATester report that her phone's SceneView is not working (apparently, her phone has a lot of problem in the code, crazy random bug not sure what's happening on iPhone XS Max).

  Now I have the scene created like this:

          let scene = SCNView()
          scene.frame = scvContainer.frame
          scene.autoresizingMask = [.flexibleWidth, .flexibleHeight]
          scene.backgroundColor = .clear
          vLayout = scene
  
          // Added to a scrollView's container 
          scvContainer.superview?.addSubview(scene)
      
      // After sometime (added the view first, then request API then wait a bit)
          scene.scene = SCNScene()
          scene.allowsCameraControl = true
          scene.antialiasingMode = .multisampling4X
          scene.preferredFramesPerSecond = 60
  
          // This is just for the sake of demonstrating the problem
          scene.scene?.rootNode.addChildNode(SCNNode(geometry: SCNSphere(radius: 50)))
  

  Then the image:

  

  I'm not able to tell what's going on since I'm also a newbie on SceneKit. The purple view is what I expect where my ScnView should display a sphere. This happened specularly on iPhone XS Max, Real Device iOS13, iPhone xs max simulator 12.4.

  I think it might be because of rendering but I have no idea how to choose the renderer. If not using sceneKit and SCNView, what other options to use to render 3d?
• How to generate valid HyperStack ImageJ data files from Matlab?

  ImageJ HyperStacks have a data type (8-32 bit), a width, a height, a number of channels, a number of slices and a number of frames. They represent 5D (XYCZT) data sets. ImageJ stores them as multipage tiff files where number of channels times number of slices times number of frames 2D (XY) images are stored. The first image seems to have two custom tags with IDs 50838 and 50839.

  I want to create tif files containing 5D data from Matlab that can be read by ImageJ as a valid 5D HyperStack.

  I can store a number of 2D images in a multipage tiff file in Matlab using imwrite(matrix, file, 'WriteMode','append') but ImageJ will read that as 3D (XYZ) image stack only. The information about the channels, slices and frames is not contained.

  I guess I could look at the ImageJ sources to find out where they store this missing information, then use Matlab's wrapper of LibTIFF to recreate the meta information of ImageJ. If you, however, already know what to do or if there is an alternative, I would like to hear it.