some issue with Apply_Bigwarp_xfm_cvsPts.groovy

[Yifan-debug]

Dear Developer,

Thank you so much for the tools, and it's very useful.
I'm currently aligning two 3D zstack tiff image with bigwrap. After alignment, I export the landmarks.
I also have several points which is aligned with Image1. I use this script(Apply_Bigwarp_xfm_cvsPts.groovy) and landmarks I export to transform these points.
However, after transformation, these points are not align well with Image2

[Yifan-debug]

Here is the picture showed two image is aligned

[bogovicj]

Hi @Yifan-debug ,

I'm glad BigWarp has been useful for you. It will be hard to help unless you give me some more information.

1. Can you confirm that this is this script you're using (https://github.com/saalfeldlab/bigwarp/blob/master/scripts/Apply_Bigwarp_Xfm_csvPts.groovy)
2. What is shown in blue for the first few images?
3. What transformation type are you using? Thin Plate spline? or Affine?
4. Are your images calibrated (i.e. do they have pixel spacing metadata). You can check with Image > Properties or Ctrl + Shift + P

[Yifan-debug]

Hi 1    Yes, this is the script I used. 2    The blue is the extra points I want to plot. 3    Thin Plate spline transform 4    The images unit is all pixel. And changed to 1 pixel [cid:e4838947-8210-4a70-91a0-ca763ee2e98d] In the first figure. the blue points are aligned well with the image 1. Then I use Thin Plate Spline to align image 1 and image 2. After that, I used this script (Apply_Bigwarp_Xfm_csvPts) to convert the extra points. Finally, I plotted the transformed_extra_points to image 2 and got the second figure. The follow-up figure showed that image 1 and image 2 are aligned well. Thank you so much for helping, Sincerely, Yifan

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________________________________ From: John Bogovic ***@***.***> Sent: Tuesday, October 15, 2024 11:27 AM To: saalfeldlab/bigwarp ***@***.***> Cc: Yifan Wang ***@***.***>; Mention ***@***.***> Subject: [EXT] Re: [saalfeldlab/bigwarp] some issue with Apply_Bigwarp_xfm_cvsPts.groovy (Issue #179) CAUTION: Email Originated Outside of Auburn. Hi @Yifan-debug<https://github.com/Yifan-debug> , I'm glad BigWarp has been useful for you. It will be hard to help unless you give me some more information. 1. Can you confirm that this is this script you're using (https://github.com/saalfeldlab/bigwarp/blob/master/scripts/Apply_Bigwarp_Xfm_csvPts.groovy) 2. What is shown in blue for the first few images? 3. What transformation type are you using? Thin Plate spline? or Affine? 4. Are your images calibrated (i.e. do they have pixel spacing metadata). You can check with Image > Properties or Ctrl + Shift + P — Reply to this email directly, view it on GitHub<#179 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ANECHKIG352EFS72WXF2LSDZ3UX43AVCNFSM6AAAAABP2PUPWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJUGMYDONRQGM>. You are receiving this because you were mentioned.