StackReg x,y translation values

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StackReg x,y translation values

Ethan Cohen


We are aligning a b/w image stack with StackReg using Rigid Transformation.

Q1: Is there a way to get the x,y, translation values out in a table for the aligned images translation coordinates relative to the reference image?

The Rigid Registration plug-in has a Euclidean transform output to a log file, but no switch on StackReg.

StackReg calls TurboReg, and I see a switch in TurboReg (hidden that does this stackOutput?).

Ethan.

Ethan Cohen, Ph.D.
Div of Biomedical Physics, WO62 Rm 1204
Office of Science and Engineering Labs,
FDA Center for Devices and Radiological Health
White Oak Federal Res Ctr.
10903 New Hampshire Ave.
Silver Spring, MD 20993
Web: http://go.usa.gov/cegV3
Office: 301-796-2485
Lab:301-796-2762
Fax: 301-796-9927
Cell: 301-538-7544

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Re: StackReg x,y translation values

Cammer, Michael-2
Maybe try this.  (No comments on quality of the bead images, please.)
http://microscopynotes.com/imagej/unwarpj/ 
This worked for a postdoc here.  Sorry not user friendly.  If the experiment had worked, we would have made a macro, but at least the registration worked.

Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016
[hidden email]  http://nyulmc.org/micros  http://microscopynotes.com/ 
Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Cohen, Ethan D
Sent: Wednesday, August 22, 2018 4:21 PM
To: [hidden email]
Subject: StackReg x,y translation values



We are aligning a b/w image stack with StackReg using Rigid Transformation.

Q1: Is there a way to get the x,y, translation values out in a table for the aligned images translation coordinates relative to the reference image?

The Rigid Registration plug-in has a Euclidean transform output to a log file, but no switch on StackReg.

StackReg calls TurboReg, and I see a switch in TurboReg (hidden that does this stackOutput?).

Ethan.

Ethan Cohen, Ph.D.
Div of Biomedical Physics, WO62 Rm 1204
Office of Science and Engineering Labs,
FDA Center for Devices and Radiological Health White Oak Federal Res Ctr.
10903 New Hampshire Ave.
Silver Spring, MD 20993
Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__go.usa.gov_cegV3&d=DwIFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=hYCgZm31m4HcgnHPxJP6t7b8l_MrbeV42nLO385PU04&s=P9PIT6fFlPMkBidV5k2m_8o5X1bC0HOih3hrb72xu8Y&e=
Office: 301-796-2485
Lab:301-796-2762
Fax: 301-796-9927
Cell: 301-538-7544

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"THIS MESSAGE FROM ETHAN COHEN IS INTENDED ONLY FOR THE USE OF THE PARTY TO WHOM IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL, AND PROTECTED FROM DISCLOSURE UNDER LAW. If you are not the addressee, or a person authorized to deliver the document to the addressee, you are hereby notified that any review, disclosure, dissemination, copying, or other action based on the content of this communication is not authorized. If you have received this document in error, please immediately notify the sender immediately by e-mail or phone."
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Re: StackReg x,y translation values

Ethan Cohen
In reply to this post by Ethan Cohen
OK, I tried a few more.

The only thing that came close was  "Register Virtual Stack Slices", selecting "Translation Only", and I get zillions of .xml files with what I think contains each individual transform.

<?xml version="1.0"?>

-<ict_transform_list>

<iict_transform data="1.5613113719003877 -7.727728562897028"--------Transform dX, dY?  class="mpicbg.trakem2.transform.TranslationModel2D" invertible="true"/>

<iict_transform data="-1.0 8.0" class="mpicbg.trakem2.transform.TranslationModel2D" invertible="true"/>

</ict_transform_list>

Must be something better out there?

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Re: StackReg x,y translation values

Philippe CARL
In reply to this post by Ethan Cohen
Dear Ethan,

Reading your post, it seems to me that that you have the same application
issues I went through and for which I have spend quite some time.
Indeed, I acquire time lapse pictures of multi positions (on 2-3 channels)
of a sample.
And from all this bunch of data I need then to correct the x-y drift seen
through the time lapse pictures on a channel and apply later on the same
corrections for all the other channels (i.e. I need as well to get out the
x-y translation values of the transformation as you requested).

For doing this job, I first (about 4 years ago) used the StackReg plugin,
until I find some experimental examples with unsolvable issues and moved
then over the JavaSIFT tool.
But I later on got as well some issues with JavaSIFT which made me look as
well for an alternative.

So now I'm using the "Template Matching and Slice Alignment" tool from
Qingzong TSENG:
https://sites.google.com/site/qingzongtseng/template-matching-ij-plugin
which up to now worked well for really all my acquired data.

Of course for all these tools (i.e. "StackReg", "JavaSIFT" and "Template
Matching and Slice Alignment") I modified the code, for at least be able to
extract the x-y translation values of the transformation.
For example for the "Template Matching and Slice Alignment" tool I'm using
now, I created the following java method:
        public static double [] getAlignSlicesDisplacement(ImagePlus _imp,
String _method, int _windowSizeX, int _windowSizeY, int _iniX, int _iniY,
int _sArea, boolean _subPixel, String _itpMethod, int _refSlice, boolean
_showRT)
which able me to get the x-y translation values of the transformation by
even short circuiting all the GUI of the plugin.

But if you want to stay with your first request, which means be able to
extract the x-y translation values of the stackreg transformation, I can
then try to dig into my old codes to see if I can get a hold of the code I
had about 4 years ago (at that time I extracted the x-y translation values
of the transformation through an Ext. feature).
Very unfortunately, as I make now a very ordered archives of all my codes
updates (which I found extremely useful in case of bugs issues) I didn't do
this about 4 years ago. So I can't make you promises whether I can easily
get a hold of the modified StackReg plugin I'm talking about.

At last, in the case you want to look in the direction of UnwarpJ as Michael
recommended you, you will find some commented details of the modification I
made for this plugin as well under:
https://forum.image.sc/t/unwarpj-scripting-documentation/2939/3

My best regards,

Philippe

Philippe CARL
Laboratoire de Bioimagerie et Pathologies
UMR 7021 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de Cohen,
Ethan D
Envoyé : mercredi 22 août 2018 22:21
À : [hidden email]
Objet : StackReg x,y translation values



We are aligning a b/w image stack with StackReg using Rigid Transformation.

Q1: Is there a way to get the x,y, translation values out in a table for the
aligned images translation coordinates relative to the reference image?

The Rigid Registration plug-in has a Euclidean transform output to a log
file, but no switch on StackReg.

StackReg calls TurboReg, and I see a switch in TurboReg (hidden that does
this stackOutput?).

Ethan.

Ethan Cohen, Ph.D.
Div of Biomedical Physics, WO62 Rm 1204
Office of Science and Engineering Labs,
FDA Center for Devices and Radiological Health White Oak Federal Res Ctr.
10903 New Hampshire Ave.
Silver Spring, MD 20993
Web: http://go.usa.gov/cegV3
Office: 301-796-2485
Lab:301-796-2762
Fax: 301-796-9927
Cell: 301-538-7544

[cid:image001.png@01D1C57E.DFA022A0]<http://www.fda.gov/>Excellent customer
service is important to us. Please take a moment to provide feedback
regarding the customer service you have received:
https://www.research.net/s/cdrhcustomerservice?O=700&D=740&B=740&E=&S=E
"THIS MESSAGE FROM ETHAN COHEN IS INTENDED ONLY FOR THE USE OF THE PARTY TO
WHOM IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED,
CONFIDENTIAL, AND PROTECTED FROM DISCLOSURE UNDER LAW. If you are not the
addressee, or a person authorized to deliver the document to the addressee,
you are hereby notified that any review, disclosure, dissemination, copying,
or other action based on the content of this communication is not
authorized. If you have received this document in error, please immediately
notify the sender immediately by e-mail or phone."
________________________________


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Re: StackReg x,y translation values

Philippe CARL
Dear Ethan,
Following my E-mail of this morning, you are lucky since I was able to get
hold of my modified version of the StackReg_ plugin I was talking about this
morning.
And here is the description I had put on top of this plugin:

| Translation_Alignment plugin corresponding to a modification of the
| StackReg_ plugin described lower.
| This plugin uses only the "translation transformation" of the
| StackReg_ plugin and applies as well a croping of the outside part
| of the shifted pictures.
| The plugin able to get the translation values of the transformation
| through the macro functions:
| Ext.getShiftValueX1
| Ext.getShiftValueX2
| Ext.getShiftValueY1
| Ext.getShiftValueY2
| Ext.getShiftValueX
| Ext.getShiftValueY

And you will be able to download this plugin under:
http://punias.free.fr/ImageJ/Translation_Alignment.java
Have a nice day,
Philippe

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de
Philippe CARL
Envoyé : jeudi 23 août 2018 10:14
À : [hidden email]
Objet : Re: StackReg x,y translation values

Dear Ethan,

Reading your post, it seems to me that that you have the same application
issues I went through and for which I have spend quite some time.
Indeed, I acquire time lapse pictures of multi positions (on 2-3 channels)
of a sample.
And from all this bunch of data I need then to correct the x-y drift seen
through the time lapse pictures on a channel and apply later on the same
corrections for all the other channels (i.e. I need as well to get out the
x-y translation values of the transformation as you requested).

For doing this job, I first (about 4 years ago) used the StackReg plugin,
until I find some experimental examples with unsolvable issues and moved
then over the JavaSIFT tool.
But I later on got as well some issues with JavaSIFT which made me look as
well for an alternative.

So now I'm using the "Template Matching and Slice Alignment" tool from
Qingzong TSENG:
https://sites.google.com/site/qingzongtseng/template-matching-ij-plugin
which up to now worked well for really all my acquired data.

Of course for all these tools (i.e. "StackReg", "JavaSIFT" and "Template
Matching and Slice Alignment") I modified the code, for at least be able to
extract the x-y translation values of the transformation.
For example for the "Template Matching and Slice Alignment" tool I'm using
now, I created the following java method:
        public static double [] getAlignSlicesDisplacement(ImagePlus _imp,
String _method, int _windowSizeX, int _windowSizeY, int _iniX, int _iniY,
int _sArea, boolean _subPixel, String _itpMethod, int _refSlice, boolean
_showRT)
which able me to get the x-y translation values of the transformation by
even short circuiting all the GUI of the plugin.

But if you want to stay with your first request, which means be able to
extract the x-y translation values of the stackreg transformation, I can
then try to dig into my old codes to see if I can get a hold of the code I
had about 4 years ago (at that time I extracted the x-y translation values
of the transformation through an Ext. feature).
Very unfortunately, as I make now a very ordered archives of all my codes
updates (which I found extremely useful in case of bugs issues) I didn't do
this about 4 years ago. So I can't make you promises whether I can easily
get a hold of the modified StackReg plugin I'm talking about.

At last, in the case you want to look in the direction of UnwarpJ as Michael
recommended you, you will find some commented details of the modification I
made for this plugin as well under:
https://forum.image.sc/t/unwarpj-scripting-documentation/2939/3

My best regards,

Philippe

Philippe CARL
Laboratoire de Bioimagerie et Pathologies
UMR 7021 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de Cohen,
Ethan D
Envoyé : mercredi 22 août 2018 22:21
À : [hidden email]
Objet : StackReg x,y translation values



We are aligning a b/w image stack with StackReg using Rigid Transformation.

Q1: Is there a way to get the x,y, translation values out in a table for the
aligned images translation coordinates relative to the reference image?

The Rigid Registration plug-in has a Euclidean transform output to a log
file, but no switch on StackReg.

StackReg calls TurboReg, and I see a switch in TurboReg (hidden that does
this stackOutput?).

Ethan.

Ethan Cohen, Ph.D.
Div of Biomedical Physics, WO62 Rm 1204
Office of Science and Engineering Labs,
FDA Center for Devices and Radiological Health White Oak Federal Res Ctr.
10903 New Hampshire Ave.
Silver Spring, MD 20993
Web: http://go.usa.gov/cegV3
Office: 301-796-2485
Lab:301-796-2762
Fax: 301-796-9927
Cell: 301-538-7544

[cid:image001.png@01D1C57E.DFA022A0]<http://www.fda.gov/>Excellent customer
service is important to us. Please take a moment to provide feedback
regarding the customer service you have received:
https://www.research.net/s/cdrhcustomerservice?O=700&D=740&B=740&E=&S=E
"THIS MESSAGE FROM ETHAN COHEN IS INTENDED ONLY FOR THE USE OF THE PARTY TO
WHOM IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED,
CONFIDENTIAL, AND PROTECTED FROM DISCLOSURE UNDER LAW. If you are not the
addressee, or a person authorized to deliver the document to the addressee,
you are hereby notified that any review, disclosure, dissemination, copying,
or other action based on the content of this communication is not
authorized. If you have received this document in error, please immediately
notify the sender immediately by e-mail or phone."
________________________________


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