HowTo wishlist

[frauzufall]

• [ ] How to loop over all images of a directory
• [ ] How to convert image types
• [ ] How to do maximum projection
• [ ] How to add overlays / work with ROIs
• [ ] How to parallelize image processing using the Executor service as done here and discussed here.
• [ ] How to measure resulting in a table (related)?
• [ ] How to deal with image calibration / pixel size in space and time?
• [ ] How to visualize a spot detection result?
• [ ] How to save an animated GIF?
• [ ] How analyse an MRI-data set of a banana slice by slice 😉
• [ ] How to react on user clicks in an image window?
• [ ] How to sychronize BigDataViewer windows/panels so that their planes are always perpendicular?
• [x] How to open confocal series zip
• [ ] How to iterate a HyperSphere in Java - I only know the cursor way.
• [ ] How to carry out pixel level mathematical operations like I can in Matlab? Full access to indices, values, logical operations etc. (may be ask @lhilbert what exactly he means by that)
• [ ] How to use the Logger?
• [ ] How to take a RandomAccessibleInterval and open it in a new or a given pre-existing BigDataViewer.
• [ ] (as a HowTo or notebook) How to do particle analysis, including (or linking to) several steps:
  • [ ] Threshold an image (this notebook)
  • [ ] Connected-component analysis (this notebook)
  • [ ] How to take an ImgLabeling and iterate over its LabelRegions
  • [ ] How to get from a LabelRegion to a RealMask (i.e. imglib2-roi)
  • [ ] How to do measurements on objects, using RealMasks sampled on an input RandomAccessibleInterval; e.g. center of mass etc.

Who has more questions?

Can others edit this post? If not, just answer and I update the list. We could also add the user handle next to a question if someone volunteers to solve a specific one-

[haesleinhuepf]

Hey @frauzufall ,

I ❤️ your initiative! There are indeed some things I've never managed in ImageJ2 and would love to learn how to do them. I link some half-backed solutions for these questions and some solutions only in ImageJ1:

• [ ] How to measure resulting in a table (related)?
• [ ] How to deal with image calibration / pixel size in space and time?
• [ ] How to visualize a spot detection result?
• [ ] How to save an animated GIF?
• [ ] How analyse an MRI-data set of a banana slice by slice 😉
• [ ] How to react on user clicks in an image window?
• [ ] How to sychronize BigDataViewer windows/panels so that their planes are always perpendicular?

Thanks again for your efforts! If you point me to better solutions answering my questions, I'm happy to help to write the HowTo-code 🎄

Cheers, Robert

[frauzufall]

Hi Robert, thanks for the questions and links, I'll look into it! Btw, here is a PR with some improvements from the discussion in the last PR https://github.com/imagej/tutorials/pull/79

Another quite straightforward thing to do would be to translate these IJ2 script templates into Java.. And sort them into the HowTos.. And vice versa. (Though I would prefer groovy) Then the HowTos would also be available from the script editor directly as templates. And if @ctrueden or someone else finds a way to do the translation automatically at some point, even better!

[haesleinhuepf]

Hey @frauzufall

Great! I'm happy to take the translation of the scripts over. For 11 files I would not invent an automatic translation algorithm ;-)

Is there a HOWTO-template and short description available of what a HOWTO-writer should take into account?

Thanks!

🐰

[frauzufall]

@haesleinhuepf cool! I added a readme and template to #79. Let me know if it's useful or needs improvement!

[haesleinhuepf]

Hey @frauzufall,

while translating the script templates, some additional questions came up:

• [x] How to open confocal series zip
• [ ] How to iterate a HyperSphere in Java - I only know the cursor way.

I may add some more while translating ;-)

[lhilbert]

How to carry out pixel level mathematical operations like I can in Matlab? Full access to indices, values, logical operations etc.

[imagejan]

@haesleinhuepf wrote:

How to iterate a HyperSphere in Java

HyperSphere<T> implements Iterable<T>, so it should work exactly as in the Jython example, no?

[haesleinhuepf]

it should work exactly as in the Jython example, no?

I couldn't find out how. My IntelliJ gives a bit a weird error message

[imagejan]

In this ImgLib2 example it seems to work.

[haesleinhuepf]

I think the problem is, neither IntelliJ nor the code writer can know what U is. A problem introduced by Java generics....

[imagejan]

neither IntelliJ nor the code writer can know what U is.

That's why you have to put U extends RealType< U > in the class/method signature, as shown in the example as well. I'd be very surprised if IntelliJ couldn't handle generics well. I'd recommend using Eclipse then ;-)

[haesleinhuepf]

That's why you have to put U extends RealType< U >

But it's DoubleType and not RealType<U>, look here: https://github.com/imagej/tutorials/blob/adding_scripting_templates/howtos/src/main/java/howto/processing/CreateAndConvolvePoints.java#L60

[imagejan]

I added a point by editing the ↗️ original post.

[ctrueden]

I merged #79, in case that affects the checklist here at all.

[frauzufall]

Thanks @ctrueden!

@haesleinhuepf, do you plan to continue with the scripts or should I continue from you branch https://github.com/imagej/tutorials/commits/adding_scripting_templates? Should we go over it together at some point?