CONFOCALMICROSCOPY Archives

November 2021

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Subject:
Re: EXT: Re: background reconstruction
From:
Aryeh Weiss <[log in to unmask]>
Reply To:
[log in to unmask]
Date:
Wed, 24 Nov 2021 21:31:58 +0200
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*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

This should do exactly what you want - It is call Nonuniform -Backgorund 
Removal
https://forum.image.sc/t/nonuniform-background-removal/26626/4
Find the link to Nonuniform_Background_Removal.jar
in the discussion thread.

It will use the regions that you define, and can fit to a plane or cubic 
surface.

Best regards
--aryeh

On 24/11/2021 19:14, Model, Michael wrote:
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Aryeh,
>
> Thank you very much, that may do it. I don't think we are prepared to buy MetaMorph
>
> Mike
>
> -----Original Message-----
> From: Aryeh Weiss <[log in to unmask]> On Behalf Of Aryeh Weiss
> Sent: Wednesday, November 24, 2021 12:06 PM
> To: Confocal Microscopy List <[log in to unmask]>
> Cc: Model, Michael <[log in to unmask]>
> Subject: EXT: Re: background reconstruction
>
> I  think that Fit_Polynomial in ImageJ might do what you want.
> https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fimagejdocu.tudor.lu%2Fplugin%2Ffilter%2Ffit_polynomial%2Fstart&amp;data=04%7C01%7Cmmodel%40kent.edu%7C732e872595ac4ede321408d9af6cab88%7Ce5a06f4a1ec44d018f73e7dd15f26134%7C1%7C0%7C637733703541644092%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=%2FMDPgn8U4y%2BFttvVHRQow4SUB55Kp%2BJokdklWOBEavs%3D&amp;reserved=0
>
> There is also a package called Gwyddion
>    https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgwyddion.net%2F&amp;data=04%7C01%7Cmmodel%40kent.edu%7C732e872595ac4ede321408d9af6cab88%7Ce5a06f4a1ec44d018f73e7dd15f26134%7C1%7C0%7C637733703541644092%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=YEMarGYQNQNWLVRBhxG659MfKBvIG4gh8TY2VUdlv%2BY%3D&amp;reserved=0
>
> That has a rich collection of leveling methods, including the ability to create a polynomial background interpolated from the masked areas only.
> It is geared towards scanning probe microscopy, but it may do what you want.
>
> best regards
> --aryeh
>
>
> On 24/11/2021 17:22, Model, Michael wrote:
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists
>> .umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy&amp;data=04%7C01%7Cm
>> model%40kent.edu%7C732e872595ac4ede321408d9af6cab88%7Ce5a06f4a1ec44d01
>> 8f73e7dd15f26134%7C1%7C0%7C637733703541644092%7CUnknown%7CTWFpbGZsb3d8
>> eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3
>> 000&amp;sdata=B7tv%2F6nIo6tNvh1kSQXsHm0dUP2fCc22j8gEN%2BY%2FvSU%3D&amp
>> ;reserved=0 Post images on
>> https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com%2F&amp;data=04%7C01%7Cmmodel%40kent.edu%7C732e872595ac4ede321408d9af6cab88%7Ce5a06f4a1ec44d018f73e7dd15f26134%7C1%7C0%7C637733703541644092%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=J6aPrizaDQyJToc1BI8OMYGIQCiX6EA41wlnNImSTFM%3D&amp;reserved=0 and include the link in your posting.
>> *****
>>
>> Dear List,
>>
>> Does anyone know how to subtract an uneven background from an image with large objects and small background area? Fully automated methods (rolling ball) would not work on such images. Ideally, I would like to manually pick a number of points that I think represent the background in various parts of the image and then run a 2D interpolation. Then the interpolated image can be subtracted from the original image. I think this problem has been resolved in Photoshop but I don't know if it works on >8 bit images.
>> Thank you!
>>
>> Mike
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: 972-3-7384051
>
> CAUTION: EXTERNAL SENDER Do not click any links, open any attachments, or REPLY to the message unless you trust the sender and know the content is safe.


-- 
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051

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