search

labsyspharm / ashlar

ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
https://labsyspharm.github.io/ashlar/
MIT License
124 stars 42 forks source link

ASHLAR #154

Open ssahoo00 opened 2 years ago

ssahoo00 commented 2 years ago

I hope someone will help me. Can we align H&E with IF image using ASHLAR.

jmuhlich commented 2 years ago

Yes, but only if A) you have individual field-of-view tile images (not a pre-stitched mosaic image), and B) the H&E and IF images were acquired on the same microscope and pixel resolution. What microscope did you use to acquire the images?

ssahoo00 commented 2 years ago

Dear Jeremy,

Thank you very much for the mail and notification.

Here are the details about images:

It is Keyence BZ-X800.

The H+E data will be .VSI files images, these are processed on the fly so there is no unstitched data.

Best Regards, Sudhakar

From: Jeremy Muhlich @.> Sent: 22 September 2022 16:14 To: labsyspharm/ashlar @.> Cc: Sudhakar Sahoo @.>; Author @.> Subject: Re: [labsyspharm/ashlar] ASHLAR (Issue #154)

Yes, but only if A) you have individual field-of-view tile images (not a pre-stitched mosaic image), and B) the H&E and IF images were acquired on the same microscope and pixel resolution. What microscope did you use to acquire the images?

— Reply to this email directly, view it on GitHubhttps://github.com/labsyspharm/ashlar/issues/154#issuecomment-1255173548, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A3GMAAAY6ONFQA7QB6BMWR3V7RZVJANCNFSM6AAAAAAQSFXEJY. You are receiving this because you authored the thread.Message ID: @.***>

jmuhlich commented 1 year ago

Sorry, Ashlar can't handle this currently. It is only designed to align images that have all been taken on the same microscope. There are camera rotation and scaling differences between different microscopes that can't be addressed using the current algorithms. Also, are your images acquired on two different tissue sections, or the same slide that was first imaged in IF and later in H&E? If they are different sections on different slides, this is also something Ashlar can't handle. In that case you can stitch the IF image using Ashlar and then use a different non-rigid slide registration tool to align the full IF and H&E images.