Re: large files

[Brandon Hurr]

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
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Ewing James]

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/>, with the link
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

[ctrueden]

Hi Jim,

Have you looked at 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

Regards,
Curtis

P.S. Regarding large files -- the ImageJ Forum (http://forum.imagej.net/)
supports attaching images up to 32MB.

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Fri, Oct 20, 2017 at 8:05 AM, Ewing James <[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/>, with the link
> 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
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Ewing James]

Thanks, Curtis. I solved this particular problem with bUnwarpJ, assigning landmarks manually.  I’ll definitely give TrakEM2 a try.
- Jim

> 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: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>

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