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petersaj / AP_histology

Histology processing
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Sagittal Slices #6

Closed Newtstein closed 2 years ago

Newtstein commented 3 years ago

Hi there!

Thanks so much for making this available for us! I was just wondering how I can incorporate images of brain slices in the sagittal plane.

Thank you for your time!

petersaj commented 3 years ago

Hi - any direction slice should work, you can just rotate the atlas to match the orientation of the slice. Have you had trouble with it?

On Sat, 14 Aug 2021 at 1:17 am Newtstein @.***> wrote:

Hi there!

Thanks so much for making this available for us! I was just wondering how I can incorporate images of brain slices in the sagittal plane.

Thank you for your time!

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Newtstein commented 3 years ago

Hi!

Thank you so much for that! It's working now!

I was also wondering whether or not I can align only a portion of the brain. For example, the images I am working with only capture the cerebellum in the sagittal plane. Is there any way this would work?

Thank you again for your immediate help!

petersaj commented 3 years ago

There's no automated way to estimate alignment to partial slices, but if you do the manual alignment step hopefully it should work alright?

On Sun, Aug 15, 2021 at 4:28 AM Newtstein @.***> wrote:

Hi!

Thank you so much for that! It's working now!

I was also wondering whether or not I can align only a portion of the brain. For example, the images I am working with only capture the cerebellum in the sagittal plane. Is there any way this would work?

Thank you again for your immediate help!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/petersaj/AP_histology/issues/6#issuecomment-898989830, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEJG4IDQR6MRUCGKMACIXXDT44X7JANCNFSM5CEPQK3Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email .

Newtstein commented 3 years ago

Hey Andy!

Thanks for that! The manual alignment step worked perfectly.

My apologies for being a novice with MATLAB, but I seem to be encountering this error and cannot figure out how to solve it. Whenever you get the chance, let me know what is wrong.

I sincerely appreciate your help.

Error:

Screen Shot 2021-08-17 at 5 04 31 PM Screen Shot 2021-08-17 at 5 07 25 PM
petersaj commented 3 years ago

That function used to come from a different repository ( https://github.com/cortex-lab/allenCCF), but it only used a few functions so I copied them over to remove the dependency.

If you pull the current repo and make sure all the folders are in the path it should work now?

On Tue, Aug 17, 2021 at 10:09 PM Newtstein @.***> wrote:

Hey Andy!

Thanks for that! The manual alignment step worked perfectly.

My apologies for being a novice with MATLAB, but I seem to be encountering this error and cannot figure out how to solve it. Whenever you get the chance, let me know what is wrong.

I sincerely appreciate your help.

Error: [image: Screen Shot 2021-08-17 at 5 04 31 PM] https://user-images.githubusercontent.com/87092669/129800399-1f7b5c52-c1ac-4e5b-a7ce-e266a944bc25.png

[image: Screen Shot 2021-08-17 at 5 07 25 PM] https://user-images.githubusercontent.com/87092669/129800777-b9e3de44-9f8d-4752-9b1d-7542903b92c9.png

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