Does Warpy can be used in script? Do you have introduction?

[HanYanxi]

I need to process lots of images. Can I use the command like run('Warpy') to use it?

[NicoKiaru]

Unfortunately, there's no easy way to batch Warpy currently, but it's on our TODO list at the facility.

It will become possible, but nothing will be done before next month. I hope to have a batch feature available by the end of 2023.

ping @romainGuiet

[HanYanxi]

Thank you! And if I have an image like this, could you give me some advice to set the parameters in the beginning?

[NicoKiaru]

Oh, whoa, these are gigantic pixels! Are you sure of these ? The object you image is 2 meters long ?

If that's correct, I would try something like:

Pixel size coarse = 800 Patch size = 40000 Pixel size precise = 80

iteration = 100 (same)

Basically everything multiplied by 80,

[HanYanxi]

It's a whole slide of fluorescent. Yes, you are right. It's impossible. Because when I followed your YouTube video. It produced the pixel width and length automatically. But I don't know the physical size of this slide. It's a problem. Can I adjust them like pixel width 0.84, and pixel length 0.84?

[HanYanxi]

Can I ask one more question about the registration process? Because I am using 2D images to register. What does the "remove images z-offset" do in the first step?

[NicoKiaru]

What does the "remove images z-offset" do in the first step?

You can keep it checked without any issue. It's a subtle issue: the planes are positioned along Z in the bio-formats library. And the z-offset can be different between the moving and the fixed image. By keeping this option checked, you make sure that the offset is ignored - which is what you want to do in 99% of the cases.

[elect86]

I need to process lots of images. Can I use the command like run('Warpy') to use it?

Maybe I may help: what kind of processing are you looking for, exactly? How do you process right now a single image and where are the images you would like to batch? All in one folder?

[NicoKiaru]

Hi @elect86 !

The batching is possible in theory but it is rather annoying right now. The Warpy wizards runs commands within commands and uses the SciJava framework to pass arguments.

The main Warpy wizard command is here:

https://github.com/BIOP/bigdataviewer-biop-tools/blob/master/src/main/java/ch/epfl/biop/scijava/command/source/register/WarpyRegisterCommand.java

And calls this command... which is doing some stuff in the UI, so not ideal for batching.

https://github.com/BIOP/bigdataviewer-biop-tools/blob/master/src/main/java/ch/epfl/biop/scijava/command/source/register/Wizard2DWholeScanRegisterCommand.java

I need to re-design these commands, or make a parallel API for easy batching. I should have known that it was bad design, even from the start... but well, here's another lesson I needed to taught myself one more time.

[HanYanxi]

What does the "remove images z-offset" do in the first step?

You can keep it checked without any issue. It's a subtle issue: the planes are positioned along Z in the bio-formats library. And the z-offset can be different between the moving and the fixed image. By keeping this option checked, you make sure that the offset is ignored - which is what you want to do in 99% of the cases.

Okay! Thank you. May I ask do you know some plugins could do remove z-offsets in imageJ?

[NicoKiaru]

May I ask do you know some plugins could do remove z-offsets in imageJ?

I'm not sure what's the context of your demand. Honestly, I don't think it's an issue you will encounteer anywhere else than in Warpy

[HanYanxi]

I need to process lots of images. Can I use the command like run('Warpy') to use it?

Maybe I may help: what kind of processing are you looking for, exactly? How do you process right now a single image and where are the images you would like to batch? All in one folder?

Hi @elect86, It looks: like I have 3 images, they are in the same folder. And I want to use Warpy to align them. But I want to do it automatically. Because I have maybe more than 5 folders.

[HanYanxi]

May I ask do you know some plugins could do remove z-offsets in imageJ?

I'm not sure what's the context of your demand. Honestly, I don't think it's an issue you will encounteer anywhere else than in Warpy

Does that mean "removing the z-offsets" and "center moving image with fixed image" are used for manual rigid registration?

[NicoKiaru]

Does that mean "removing the z-offsets" and "center moving image with fixed image" are used for manual rigid registration?

Both options are there to help with the initial state. There are not used per se for the registration. It's just that if the images are not overlapping at all when you start the registration process, the wizard will just not work. So, initially, you just want to re-center both images. That's what these options are for. It's just there to help at the beginning of the registration process.

You can just experiment and see what happens if you disable them.

[HanYanxi]

Does that mean "removing the z-offsets" and "center moving image with fixed image" are used for manual rigid registration?

Both options are there to help with the initial state. There are not used per se for the registration. It's just that if the images are not overlapping at all when you start the registration process, the wizard will just not work. So, initially, you just want to re-center both images. That's what these options are for. It's just there to help at the beginning of the registration process.

You can just experiment and see what happens if you disable them.

Okay! Thank you so much for your reply!

[HanYanxi]

Can I ask a question about Warpy registration? When I start registration, it shows these errors, and I can't export the registered images using "export warpy registered image".

[NicoKiaru]

Yeah, the export from Warpy is indeed broken currently, sorry. I've opened an issue (https://github.com/BIOP/bigdataviewer-biop-tools/issues/55).

The current alternative is to export from QuPath, cf:

https://forum.image.sc/t/saving-to-ome-tiff-slow-warpy-and-qupath/69153

[HanYanxi]

Yeah, the export from Warpy is indeed broken currently, sorry. I've opened an issue (BIOP/bigdataviewer-biop-tools#55).

The current alternative is to export from QuPath, cf:

https://forum.image.sc/t/saving-to-ome-tiff-slow-warpy-and-qupath/69153

okay, thank you. When I did registration it also shows errors.

[NicoKiaru]

Is Fiji up to date ? Do you have elastix 5.0.1 ( and not elastix 5.1.0 ) ?

Please check the script refered in https://biop.github.io/ijp-imagetoatlas/#i-cant-start-any-elastix-registrations

And make sure that you select 'MILLIMETER' when importing the QuPath project

[HanYanxi]

the folders are like this, I didn't change them.

[NicoKiaru]

Ah, ok.

Could you try to run the test script mention in the link I've sent above and let me know how that goes ?