Error when overlay atlas slice onto histological image

[Virginia9733]

Hi there,

It is so great to use HERBS!
I have successfully had a 3D trajectory track of NP1.0 from sagittal slices, great!

However, during the process, I encountered some issues when trying to overlay the atlas slice onto the histological image.

1. Error when removing the background.
   When I choose the color black and click on the black background with thresholds 1-20, it does not capture the contour of the slices. When I choose blue and use threshold 10 to create a mask, then delete or backspace would not clear the selected regions either.
   

2. Error when erasing background
   I chose the black color to erase the background, but nothing changes.
   

3. Error when overlaying atlas slice onto histological image
   I can't press button H to mapping the segmentation of atlas to the histological image, after I transform to atlas and press acccept.
   

[JingyiGF]

Hi, thanks for the feedback. May I know the purpose to match atlas slice onto histological images? The original design goal of doing so was to help anatomists to segment brain regions on each histological slice, and merge all histological slices into 3d volume. It is still under development ( I think I wrote it in the cook book, but I might be wrong. Too busy to remember everything) ;-)

[Virginia9733]

Thank you for your reply! Yes, I understand that it’s still under development! The purpose of doing this is exactly want to create 3 D reconstruction of the brain. Also, I am not quite sure about how to deal with multiple slices. But I guess currently my priority is to figure out how to properly clean the background and erase unnecessary stuff of the slice. Many thanks! Get Outlook for iOS<https://aka.ms/o0ukef>

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________________________________ From: Jingyi G. Fuglstad ***@***.***> Sent: Friday, October 28, 2022 1:19:56 AM To: JingyiGF/HERBS ***@***.***> Cc: Muhang Li ***@***.***>; Author ***@***.***> Subject: Re: [JingyiGF/HERBS] Error when overlay atlas slice onto histological image (Issue #22) Hi, thanks for the feedback. May I know the purpose to match atlas slice onto histological images? The original design goal of doing so was to help anatomists to segment brain regions on each histological slice, and merge all histological slices into 3d volume. It is still under development ( I think I wrote it in the cook book, but I might be wrong. Too busy to remember everything) ;-) — Reply to this email directly, view it on GitHub<#22 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AOVPEIXRTMI6NJGCNGYS3QLWFKTSZANCNFSM6AAAAAARQE44XU>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[JingyiGF]

ok, I see. the magic wand is nice when the image has white background (here I mean image background, not HERBS background. In View menu you can change '2d Mode', then you will see what I mean with image background and HERBS background.) but you have a black background image. So the easiest way to remove the unnecessary part is to use polygon lasso tool. In CookBook 6.7.1, there is a small part on how to use lasso tool. you can have a look first and play around a bit. I will write a more clear tutorial on it tomorrow. Remember if you want to delete something on img-process layer, you need to active the layer (clicking on it to make it in light gray).