Thanks, Curtis. I solved this particular problem with bUnwarpJ, assigning landmarks manually. I’ll definitely give TrakEM2 a try.
> On Oct 30, 2017, at 2:53 PM, Curtis Rueden <
[hidden email]> wrote:
>
> Hi Jim,
>
> Have you looked at TrakEM2?
https://imagej.net/TrakEM2 <
https://imagej.net/TrakEM2>
>
> It supports both automatic and manual image registration, including the
> case where you need to correct for distorted tissue. The video tutorials
> might be useful:
>
https://imagej.net/TrakEM2_tutorials <
https://imagej.net/TrakEM2_tutorials>
>
> Regards,
> Curtis
>
> P.S. Regarding large files -- the ImageJ Forum (
http://forum.imagej.net/ <
http://forum.imagej.net/>)
> supports attaching images up to 32MB.
>
> --
> Curtis Rueden
> LOCI software architect -
https://loci.wisc.edu/software <
https://loci.wisc.edu/software>
> ImageJ2 lead, Fiji maintainer -
https://imagej.net/User:Rueden <
https://imagej.net/User:Rueden>
> Did you know ImageJ has a forum?
http://forum.imagej.net/ <
http://forum.imagej.net/>
>
>
> On Fri, Oct 20, 2017 at 8:05 AM, Ewing James <
[hidden email] <mailto:
[hidden email]>>
> wrote:
>
>> Thanks for the tip.
>> I’m trying to register two files, the first an undistorted image a rat
>> brain, and the second a distorted tissue slice of approximately the same
>> slice. I put the two files are on box.com <
http://box.com/> <
http://box.com/ <
http://box.com/>>, with the link
>>
https://app.box.com/s/cfrh9iwh1i7frjtz40j0n46icbhm1rke <
https://app.box.com/s/cfrh9iwh1i7frjtz40j0n46icbhm1rke> <
>>
https://app.box.com/s/cfrh9iwh1i7frjtz40j0n46icbhm1rke>
>>
>> The first file is tagged slice.tif, and the second is
>> PS02C_H&E_1x.jpg.tif. First file is an MRI image, second is an H&E tissue
>> slice. I want to morph the H&E slide to the MRI.
>>
>> In Fiji, I tried Plugins>Registration>Register Virtual Stack Slices, and
>> bUnbwarpJ, with no apparent success. Plugins>Landmarks>Name Landmarks and
>> Register seemed like it should work, but generated a map of 0’s with the
>> legend at the top saying “Transformed (33%)” when I tried the thin-plate
>> spline registration algorithm. I would bet that there are a number of users
>> out there who have solved this problem. Any hints? Thanks in advance.
>>
>> - Jim Ewing
>>
>>
>>> On Oct 19, 2017, at 11:29 AM, Brandon Hurr <
[hidden email]>
>> wrote:
>>>
>>> Put them on Dropbox or Google Drive and provide a public link in your
>>> message.
>>>
>>> How big are we talking? gDrive takes up to 2 GB file size I believe.
>>>
>>> HTH,
>>> B
>>>
>>> On Thu, Oct 19, 2017 at 8:04 AM, Ewing James <
[hidden email]
>>>
>>> wrote:
>>>
>>>> Dear List -
>>>>
>>>> I have two large files that I’d like some advice on co-registering. Is
>>>> there some place that I can drop these files? The list server won’t
>> let me
>>>> attach either one to this message.
>>>>
>>>> - Jim Ewing
>>>> --
>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>>
>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html <
http://imagej.nih.gov/ij/list.html>
>>
>
> --
> ImageJ mailing list:
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