fix the position of images

[中村 宗一]

Hi

I took serial images of serial slices of a whole cell to obtain 3D images, but some images were out of position because the cell moved slightly. Please help me. Is there a program or plugin to fix the positions of images properly.

Soichi

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[Cameron Nowell-2]

Hi Soichi,

The simplest way is to use StackReg

http://bigwww.epfl.ch/thevenaz/stackreg/

for trickier alignments you can use SIFT alignment

http://fly.mpi-cbg.de/~saalfeld/Projects/javasift.html


both of these are built into the Fiji distribution of ImageJ (www.fiji.sc)


Cheers

Cam




Cameron J. Nowell
Research Facilities Manager

Monash Institute of Pharmaceutical Sciences
Monash University
399 Royal Parade
(Mail address: 381 Royal Parade)
Parkville, VIC, 3052
Australia

Email: [hidden email]
Mobile: [phone]
Office: [phone]

LinkedIn: Profile
Research Gate:  Profile




-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of ?? ??
Sent: Tuesday, 20 August 2013 2:56 PM
To: [hidden email]
Subject: fix the position of images

Hi

I took serial images of serial slices of a whole cell to obtain 3D images, but some images were out of position because the cell moved slightly. Please help me. Is there a program or plugin to fix the positions of images properly.

Soichi

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

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

[中村 宗一]

Hi Cam,

Thank very much. Stackreg works very well.

Soichi,




----- Original Message -----

>> From: Cameron Nowell <[hidden email]>
>> To: <[hidden email]>
>> Date: 2013-08-20 14:53:28
>> Subject: Re: fix the position of images
>>
>> Hi Soichi,
>>
>> The simplest way is to use StackReg
>>
>> http://bigwww.epfl.ch/thevenaz/stackreg/
>>
>> for trickier alignments you can use SIFT alignment
>>
>> http://fly.mpi-cbg.de/~saalfeld/Projects/javasift.html
>>
>>
>> both of these are built into the Fiji distribution of ImageJ (www.fiji.sc)
>>
>>
>> Cheers
>>
>> Cam
>>
>>
>>
>>
>> Cameron J. Nowell
>> Research Facilities Manager
>>
>> Monash Institute of Pharmaceutical Sciences
>> Monash University
>> 399 Royal Parade
>> (Mail address: 381 Royal Parade)
>> Parkville, VIC, 3052
>> Australia
>>
>> Email: [hidden email]
>> Mobile: [phone]
>> Office: [phone]
>>
>> LinkedIn: Profile
>> Research Gate:  Profile
>>
>>
>>
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of ?? ??
>> Sent: Tuesday, 20 August 2013 2:56 PM
>> To: [hidden email]
>> Subject: fix the position of images
>>
>> Hi
>>
>> I took serial images of serial slices of a whole cell to obtain 3D images, but some images were out of position because the cell moved slightly. Please help me. Is there a program or plugin to fix the positions of images properly.
>>
>> Soichi
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>

中村宗一
電話：[phone]
903-0213
沖縄県西原町千原1番地
琉球大学理学部海洋自然科学科生物系
熱帯生命機能学講座

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

[Cameron Nowell-2]

Just be careful which transform you use. For what you captured Translation should be all you need. Any of the other ones are going to rotate, scale and warp your image.




-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of ?? ??
Sent: Tuesday, 20 August 2013 5:03 PM
To: [hidden email]
Subject: Re: fix the position of images

Hi Cam,

Thank very much. Stackreg works very well.

Soichi,




----- Original Message -----

>> From: Cameron Nowell <[hidden email]>
>> To: <[hidden email]>
>> Date: 2013-08-20 14:53:28
>> Subject: Re: fix the position of images
>>
>> Hi Soichi,
>>
>> The simplest way is to use StackReg
>>
>> http://bigwww.epfl.ch/thevenaz/stackreg/
>>
>> for trickier alignments you can use SIFT alignment
>>
>> http://fly.mpi-cbg.de/~saalfeld/Projects/javasift.html
>>
>>
>> both of these are built into the Fiji distribution of ImageJ
>> (www.fiji.sc)
>>
>>
>> Cheers
>>
>> Cam
>>
>>
>>
>>
>> Cameron J. Nowell
>> Research Facilities Manager
>>
>> Monash Institute of Pharmaceutical Sciences Monash University
>> 399 Royal Parade
>> (Mail address: 381 Royal Parade)
>> Parkville, VIC, 3052
>> Australia
>>
>> Email: [hidden email]
>> Mobile: [phone]
>> Office: [phone]
>>
>> LinkedIn: Profile
>> Research Gate:  Profile
>>
>>
>>
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of ?? ??
>> Sent: Tuesday, 20 August 2013 2:56 PM
>> To: [hidden email]
>> Subject: fix the position of images
>>
>> Hi
>>
>> I took serial images of serial slices of a whole cell to obtain 3D images, but some images were out of position because the cell moved slightly. Please help me. Is there a program or plugin to fix the positions of images properly.
>>
>> Soichi
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>

中村宗一
電話：[phone]
903-0213
沖縄県西原町千原1番地
琉球大学理学部海洋自然科学科生物系
熱帯生命機能学講座

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

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