Advice petition on learning java programming

[Soriano.Joaquim]

Hi there!

I'm an imagej user. I am able to write my own macros so far by using the macro recorder.

I'm thinking of doing the next step which I think might be learning java programming.

Can anyone give me some advice about which is the best way to do so? I mean:  to join an in-person "x" course or "x" internet course or learning on my own with "x" material, don't even try it is painfully hard and useless, ...

Thank you very much in advance.

 

Joaquim Soriano Felipe.

Confocal Microscopy Unit

Spanish National Cancer Research Centre (CNIO)

Melchor Fernández Almagro,3, E-28029 Madrid, Spain

Phone  + 34 917 328 000, exts.: 3161, 3162. [hidden email] <mailto:[hidden email]>

 



**NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

[Bill Mohler]

I used "Java All-in-one Desk Reference FOR DUMMIES" by Lowe and Burd to
learn basics of the language.  Very well explained and not too many
typos (but just enough to keep you on your toes!).  Then I just started
reading and playing with others' ImageJ plugin code.  I now have a
reasonably workable ability to create my own plugins.  Still feel I
could benefit from a real class in object-oriented programming in general...

Bill

Soriano.Joaquim wrote:

> Hi there!
>
> I'm an imagej user. I am able to write my own macros so far by using the macro recorder.
>
> I'm thinking of doing the next step which I think might be learning java programming.
>
> Can anyone give me some advice about which is the best way to do so? I mean:  to join an in-person "x" course or "x" internet course or learning on my own with "x" material, don't even try it is painfully hard and useless, ...
>
> Thank you very much in advance.
>
>  
>
> Joaquim Soriano Felipe.
>
> Confocal Microscopy Unit
>
> Spanish National Cancer Research Centre (CNIO)
>
> Melchor Fernández Almagro,3, E-28029 Madrid, Spain
>
> Phone  + 34 917 328 000, exts.: 3161, 3162. [hidden email] <mailto:[hidden email]>
>
>  
>
>
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>
>
>
>  

[dscho]

Hi,

On Wed, 11 Aug 2010, Soriano.Joaquim wrote:

> I'm thinking of doing the next step which I think might be learning java
> programming.
>
> Can anyone give me some advice about which is the best way to do so?

If you like to learn from online resources, you might be happy with

        http://www.vogella.de/articles/JavaIntroduction/article.html

If you find it hard to learn Java from that site, just Google for
"introduction java", and you will find quite a handful of other options.

Ciao,
Johannes

[simon andrews (BI)]

On 11 Aug 2010, at 16:28, Soriano.Joaquim wrote:

> Hi there!
>
> I'm an imagej user. I am able to write my own macros so far by using the macro recorder.
>
> I'm thinking of doing the next step which I think might be learning java programming.
>
> Can anyone give me some advice about which is the best way to do so? I mean:  to join an in-person "x" course or "x" internet course or learning on my own with "x" material, don't even try it is painfully hard and useless, ...

To some extent this will depend on how you find you learn best.  I picked up Java from the O'Reilly 'Learning Java' book and then just by playing around writing my own programs.  Other people seem to hate learning from books and are much happier with a hands on course.

One thing I would advise is to see if you can find someone near you who already knows java pretty well and get them to look through anything you've written.  Having someone to ask when you don't get something is invaluable, as is getting the perspective of how someone else would have approached a problem.

Good luck!

Simon.

[GAUTAM SHANKAR]

http://www.youtube.com/watch?v=Hl-zzrqQoSE&feature=PlayList&p=FE2CE09D83EE3E28&index=1


youtube tutorials were my way.. I didn't have a chance to take actual java
classes in college, except higher level software engineering courses
required that I know it. So this tutorial helped me.
It's good hands on tutorial, it won't give you concrete knowledge that you
would need to know to answer interview questions for example.



On Wed, Aug 11, 2010 at 8:38 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Wed, 11 Aug 2010, Soriano.Joaquim wrote:
>
> > I'm thinking of doing the next step which I think might be learning java
> > programming.
> >
> > Can anyone give me some advice about which is the best way to do so?
>
> If you like to learn from online resources, you might be happy with
>
>        http://www.vogella.de/articles/JavaIntroduction/article.html
>
> If you find it hard to learn Java from that site, just Google for
> "introduction java", and you will find quite a handful of other options.
>
> Ciao,
> Johannes
>

[David Webster]

If you have experience programming in something like C, then chapters 2 and
3 in the e-book "Thinking in Java" by Bruce Eckel probably can get you
started for ImageJ programming. At least its  free.

A caution though. the way you use methods as opposed to functions seems
a little odd if your experience with programming is not object oriented.
Also, since things like images are actually references, changing pixel
values inside of a method wilkl change them outside of the method as well.

Have Fun David Webster

On Wed, Aug 11, 2010 at 8:28 AM, Soriano.Joaquim <[hidden email]> wrote:

> Hi there!
>
> I'm an imagej user. I am able to write my own macros so far by using the
> macro recorder.
>
> I'm thinking of doing the next step which I think might be learning java
> programming.
>
> Can anyone give me some advice about which is the best way to do so? I
> mean:  to join an in-person "x" course or "x" internet course or learning on
> my own with "x" material, don't even try it is painfully hard and useless,
> ...
>
> Thank you very much in advance.
>
>
>
> Joaquim Soriano Felipe.
>
> Confocal Microscopy Unit
>
> Spanish National Cancer Research Centre (CNIO)
>
> Melchor Fernández Almagro,3, E-28029 Madrid, Spain
>
> Phone  + 34 917 328 000, exts.: 3161, 3162. [hidden email] <mailto:
> [hidden email]>
>
>
>
>
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los
> ficheros adjuntos, pueden contener informaciÿn protegida para el uso
> exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o
> cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el
> destinatario. Si usted recibe por error este correo, se ruega comunicarlo al
> remitente y borrar el mensaje recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may
> contain confidential and privileged information for the sole use of the
> designated recipient named above. Distribution, reproduction or any other
> use of this transmission by any party other than the intended recipient is
> prohibited. If you are not the intended recipient please contact the sender
> and delete all copies.
>
>
>

[Joseph Mist]

I learned the basics of Java with this book (I used the 3rd edition)
http://www.bluej.org/objects-first/
I think that this is the best text I have ever learned from (though I did have a series of lectures to go with it). The BlueJ software is free and easy to use. It is worth looking at even if you don't buy the book.
You may also like to consider the Image Processing text written with ImageJ in mind.
http://www.imagingbook.com/
Though you may already be familiar with the Image Processing content of the book if you have studied Image Processing before.
Another useful resource for writing ImageJ plugins is
http://www.imagingbook.com/fileadmin/goodies/ijtutorial/tutorial171.pdf
It may be that you would like to dabble with existing plugins so that you learn the bits of Java that are immediately relevent without having to learn the other stuff. You would probably still need to Java in the long run bit this would provide a more "hands on" start and enable you to start writing plugins straight away.
Joe

[Bertrand Vernay]

Hi Joaquim

I have also started to learn a bit about Java.

I'm using the previously mentioned Youtube tutorial
http://www.youtube.com/watch?v=Hl-zzrqQoSE&feature=PlayList&p=FE2CE09D83EE3E
28&index=1

and the Open University material (free access)
http://computing.open.ac.uk/m254/

Bertrand

--
Dr Bertrand Vernay
Microscopy Senior Research Associate
Developmental Biology Unit
UCL Institute of Child Health
30 Guilford Street
London WC1N 1EH, UK

Tel :  (+44)  020 7905 2224 (direct line)
       (+44)  020 7242 9789 (ICH switchboard)

Fax:    (+44)  020 7831 4366

E-mail: [hidden email]

http://www.ich.ucl.ac.uk/services_and_facilities/lab_services/confocal_micro
scopy_core_facility/index.html
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of GAUTAM
SHANKAR
Sent: 11 August 2010 17:17
To: [hidden email]
Subject: Re: Advice petition on learning java programming

http://www.youtube.com/watch?v=Hl-zzrqQoSE&feature=PlayList&p=FE2CE09D83EE3E
28&index=1


youtube tutorials were my way.. I didn't have a chance to take actual java
classes in college, except higher level software engineering courses
required that I know it. So this tutorial helped me.
It's good hands on tutorial, it won't give you concrete knowledge that you
would need to know to answer interview questions for example.



On Wed, Aug 11, 2010 at 8:38 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Wed, 11 Aug 2010, Soriano.Joaquim wrote:
>
> > I'm thinking of doing the next step which I think might be learning java
> > programming.
> >
> > Can anyone give me some advice about which is the best way to do so?
>
> If you like to learn from online resources, you might be happy with
>
>        http://www.vogella.de/articles/JavaIntroduction/article.html
>
> If you find it hard to learn Java from that site, just Google for
> "introduction java", and you will find quite a handful of other options.
>
> Ciao,
> Johannes
>

[Jacqueline Ross]

Dear All,

One of our users has acquired time-lapse data on a Nikon BioStation that
she now wants to merge into a movie. She has acquired 3 images at each
time point, which can be merged together nicely using the 2D Stitch
plugin.

However, there are over 1000 sets of images ("top", "middle" and
"bottom") to be merged.

Is anyone able to let me know how I can put this into a macro? We have 3
data sets of tiff files sequentially named in 3 individual folders, top,
middle and bottom. The tiling is not straightforward in that it is like
a zigzag rather than a rectangle. However, the 2D plugin did merge the 3
images very well so if we can automate the procedure and obtain the
merged tiff files for each time point, we can then easily build the AVI.

I have looked at the batch processing options but I haven't figured out
how to select the correct images.

Thanks in advance for any assistance.

Kind regards,

Jacqui

Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/

[Stephan Preibisch]

Hi,

you should be able to record a macro that stores what allowed you to merge
it for one timepoint. In the ideal case you simple make a loop over the 1000
images and it should be fine. At which point are you stuck?

Nice greetings,
Stephan

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Jacqui Ross
> Sent: Montag, 15. November 2010 21:53
> To: [hidden email]
> Subject: FIJI 2D stitching in a macro
>
> Dear All,
>
> One of our users has acquired time-lapse data on a Nikon BioStation
> that
> she now wants to merge into a movie. She has acquired 3 images at each
> time point, which can be merged together nicely using the 2D Stitch
> plugin.
>
> However, there are over 1000 sets of images ("top", "middle" and
> "bottom") to be merged.
>
> Is anyone able to let me know how I can put this into a macro? We have
> 3
> data sets of tiff files sequentially named in 3 individual folders,
> top,
> middle and bottom. The tiling is not straightforward in that it is like
> a zigzag rather than a rectangle. However, the 2D plugin did merge the
> 3
> images very well so if we can automate the procedure and obtain the
> merged tiff files for each time point, we can then easily build the
> AVI.
>
> I have looked at the batch processing options but I haven't figured out
> how to select the correct images.
>
> Thanks in advance for any assistance.
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
>
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland, NEW ZEALAND
>
> Tel: [phone] Ext 87438
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/

[Jacqueline Ross]

Hi Stephan,

Thanks for your fast reply. At the moment, all I can do is get the first
2 images to fuse and that image is saved into my "Tiled" folder.
However, that image then needs to be merged with the file called
"bottom" but I get an error then as shown below:

Numeric value expected in run() function
Dialog box title: "Stitching of 2D Images"
Key: "fusion alpha"
Value or variable name" "Linear Blending"


The macro I have recorded is as below;

open("C:\\Documents and Settings\\jros013\\Desktop\\Copy of
test\\top\\top001.tif"); open("C:\\Documents and
Settings\\jros013\\Desktop\\Copy of test\\middle\\middle001.tif");
open("C:\\Documents and Settings\\jros013\\Desktop\\Copy of
test\\bottom\\bottom001.tif"); run("2D Stitching", "first=top001.tif
_use_channel_for_first=[Red, Green and Blue] second=middle001.tif
use_channel_for_second=[Red, Green and Blue] use how=5 create
_fusion=[Linear Blending] fusion=1.50
fused=Fused_top001.tif_middle001.tif compute_overlap x=0 y=0"); run("2D
Stitching", "first=Fused_top001.tif_middle001.tif
use_channel_for_first=[Red, Green and Blue] second=bottom001.tif
use_channel_for_second=[Red, Green and Blue] use how=5 create
fusion=[Linear Blending] fusion=1.50
fused=Fused_top001.tif_middle001.tif compute_overlap x=0 y=0");
saveAs("Tiff", "C:\\Documents and Settings\\jros013\\Desktop\\Copy of
test\\Tiled\\Fused_top001.tif_middle001.tif");
close();

I will also need to change the naming and make it generic so that it
sequentially goes through all of the images in the folders in order and
creates a tiled image from each one. I guess this is what you mean by a
"simple loop"? I'm not sure how to do that for multiple folders. I then
want to create the AVI from those tiled images.

If you can assist with working out what is causing the error, it would
be much appreciated.

Kind regards,

Jacqui

Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: Stephan Preibisch [mailto:[hidden email]]
Sent: Tuesday, 16 November 2010 2:03 p.m.
To: 'ImageJ Interest Group'
Cc: Jacqui Ross
Subject: RE: FIJI 2D stitching in a macro

Hi,

you should be able to record a macro that stores what allowed you to
merge it for one timepoint. In the ideal case you simple make a loop
over the 1000 images and it should be fine. At which point are you
stuck?

Nice greetings,
Stephan

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Jacqui Ross
> Sent: Montag, 15. November 2010 21:53
> To: [hidden email]
> Subject: FIJI 2D stitching in a macro
>
> Dear All,
>
> One of our users has acquired time-lapse data on a Nikon BioStation
> that she now wants to merge into a movie. She has acquired 3 images at

> each time point, which can be merged together nicely using the 2D
> Stitch plugin.
>
> However, there are over 1000 sets of images ("top", "middle" and
> "bottom") to be merged.
>
> Is anyone able to let me know how I can put this into a macro? We have
> 3
> data sets of tiff files sequentially named in 3 individual folders,
> top, middle and bottom. The tiling is not straightforward in that it
> is like a zigzag rather than a rectangle. However, the 2D plugin did
> merge the
> 3
> images very well so if we can automate the procedure and obtain the
> merged tiff files for each time point, we can then easily build the
> AVI.
>
> I have looked at the batch processing options but I haven't figured
> out how to select the correct images.
>
> Thanks in advance for any assistance.
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
>
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland, NEW ZEALAND
>
> Tel: [phone] Ext 87438
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/

[Stephan Preibisch]

Hi,

when did you record this macro? Very recently, there was a bug fixed in the
Macro recording of the 2d-stitching where the field names were slightly
modified, it seems you still have the old field names...might that be the
case? Then simply re-recording should solve the problem.

Nice greetings,
Stephan

> -----Original Message-----
> From: Jacqui Ross [mailto:[hidden email]]
> Sent: Dienstag, 16. November 2010 05:02
> To: ImageJ Interest Group
> Cc: Stephan Preibisch
> Subject: RE: FIJI 2D stitching in a macro
>
> Hi Stephan,
>
> Thanks for your fast reply. At the moment, all I can do is get the
> first
> 2 images to fuse and that image is saved into my "Tiled" folder.
> However, that image then needs to be merged with the file called
> "bottom" but I get an error then as shown in the attached document.
>
> In case the attachment doesn't come through, the error states as below:
>
> Numeric value expected in run() function Dialog box title: "Stitching
> of 2D Images"
> Key: "fusion alpha"
> Value or variable name" "Linear Blending"
>
>
> The macro I have recorded is as below;
>
> open("C:\\Documents and Settings\\jros013\\Desktop\\Copy of
> test\\top\\top001.tif"); open("C:\\Documents and
> Settings\\jros013\\Desktop\\Copy of test\\middle\\middle001.tif");
> open("C:\\Documents and Settings\\jros013\\Desktop\\Copy of
> test\\bottom\\bottom001.tif"); run("2D Stitching", "first=top001.tif
> _use_channel_for_first=[Red, Green and Blue] second=middle001.tif
> use_channel_for_second=[Red, Green and Blue] use how=5 create
> _fusion=[Linear Blending] fusion=1.50
> fused=Fused_top001.tif_middle001.tif compute_overlap x=0 y=0"); run("2D
> Stitching", "first=Fused_top001.tif_middle001.tif
> use_channel_for_first=[Red, Green and Blue] second=bottom001.tif
> use_channel_for_second=[Red, Green and Blue] use how=5 create
> fusion=[Linear Blending] fusion=1.50
> fused=Fused_top001.tif_middle001.tif compute_overlap x=0 y=0");
> saveAs("Tiff", "C:\\Documents and Settings\\jros013\\Desktop\\Copy of
> test\\Tiled\\Fused_top001.tif_middle001.tif");
> close();
>
> I will also need to change the naming and make it generic so that it
> sequentially goes through all of the images in the folders in order and
> creates a tiled image from each one. I then want to create the AVI from
> those tiled images.
>
> If you can assist with working out what is causing the error, it would
> be much appreciated.
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
>
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland, NEW ZEALAND
>
> Tel: [phone] Ext 87438
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>
>
> -----Original Message-----
> From: Stephan Preibisch [mailto:[hidden email]]
> Sent: Tuesday, 16 November 2010 2:03 p.m.
> To: 'ImageJ Interest Group'
> Cc: Jacqui Ross
> Subject: RE: FIJI 2D stitching in a macro
>
> Hi,
>
> you should be able to record a macro that stores what allowed you to
> merge it for one timepoint. In the ideal case you simple make a loop
> over the 1000 images and it should be fine. At which point are you
> stuck?
>
> Nice greetings,
> Stephan
>
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> > Jacqui Ross
> > Sent: Montag, 15. November 2010 21:53
> > To: [hidden email]
> > Subject: FIJI 2D stitching in a macro
> >
> > Dear All,
> >
> > One of our users has acquired time-lapse data on a Nikon BioStation
> > that she now wants to merge into a movie. She has acquired 3 images
> at
> > each time point, which can be merged together nicely using the 2D
> > Stitch plugin.
> >
> > However, there are over 1000 sets of images ("top", "middle" and
> > "bottom") to be merged.
> >
> > Is anyone able to let me know how I can put this into a macro? We
> have
> > 3
> > data sets of tiff files sequentially named in 3 individual folders,
> > top, middle and bottom. The tiling is not straightforward in that it
> > is
> like
> > a zigzag rather than a rectangle. However, the 2D plugin did merge
> the
> > 3
> > images very well so if we can automate the procedure and obtain the
> > merged tiff files for each time point, we can then easily build the
> > AVI.
> >
> > I have looked at the batch processing options but I haven't figured
> out
> > how to select the correct images.
> >
> > Thanks in advance for any assistance.
> >
> > Kind regards,
> >
> > Jacqui
> >
> > Jacqueline Ross
> >
> > Biomedical Imaging Microscopist
> > Biomedical Imaging Research Unit
> > School of Medical Sciences
> > Faculty of Medical & Health Sciences
> > The University of Auckland
> > Private Bag 92019
> > Auckland, NEW ZEALAND
> >
> > Tel: [phone] Ext 87438
> > Fax: [phone]
> >
> > http://www.fmhs.auckland.ac.nz/sms/biru/

[Jacqueline Ross]

Hi Stephan,

I have updated my Fiji version and still got the same results
unfortunately.

Thanks.

Kind regards,

Jacqui

Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: Stephan Preibisch [mailto:[hidden email]]
Sent: Tuesday, 16 November 2010 10:16 p.m.
To: Jacqui Ross; 'ImageJ Interest Group'
Subject: RE: FIJI 2D stitching in a macro

Hi,

when did you record this macro? Very recently, there was a bug fixed in
the
Macro recording of the 2d-stitching where the field names were slightly
modified, it seems you still have the old field names...might that be
the
case? Then simply re-recording should solve the problem.

Nice greetings,
Stephan

> -----Original Message-----
> From: Jacqui Ross [mailto:[hidden email]]
> Sent: Dienstag, 16. November 2010 05:02
> To: ImageJ Interest Group
> Cc: Stephan Preibisch
> Subject: RE: FIJI 2D stitching in a macro
>
> Hi Stephan,
>
> Thanks for your fast reply. At the moment, all I can do is get the
> first
> 2 images to fuse and that image is saved into my "Tiled" folder.
> However, that image then needs to be merged with the file called
> "bottom" but I get an error then as shown in the attached document.
>
> In case the attachment doesn't come through, the error states as

below:

>
> Numeric value expected in run() function Dialog box title: "Stitching
> of 2D Images"
> Key: "fusion alpha"
> Value or variable name" "Linear Blending"
>
>
> The macro I have recorded is as below;
>
> open("C:\\Documents and Settings\\jros013\\Desktop\\Copy of
> test\\top\\top001.tif"); open("C:\\Documents and
> Settings\\jros013\\Desktop\\Copy of test\\middle\\middle001.tif");
> open("C:\\Documents and Settings\\jros013\\Desktop\\Copy of
> test\\bottom\\bottom001.tif"); run("2D Stitching", "first=top001.tif
> _use_channel_for_first=[Red, Green and Blue] second=middle001.tif
> use_channel_for_second=[Red, Green and Blue] use how=5 create
> _fusion=[Linear Blending] fusion=1.50
> fused=Fused_top001.tif_middle001.tif compute_overlap x=0 y=0");

run("2D

> Stitching", "first=Fused_top001.tif_middle001.tif
> use_channel_for_first=[Red, Green and Blue] second=bottom001.tif
> use_channel_for_second=[Red, Green and Blue] use how=5 create
> fusion=[Linear Blending] fusion=1.50
> fused=Fused_top001.tif_middle001.tif compute_overlap x=0 y=0");
> saveAs("Tiff", "C:\\Documents and Settings\\jros013\\Desktop\\Copy of
> test\\Tiled\\Fused_top001.tif_middle001.tif");
> close();
>
> I will also need to change the naming and make it generic so that it
> sequentially goes through all of the images in the folders in order

and
> creates a tiled image from each one. I then want to create the AVI
from

> those tiled images.
>
> If you can assist with working out what is causing the error, it would
> be much appreciated.
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
>
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland, NEW ZEALAND
>
> Tel: [phone] Ext 87438
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>
>
> -----Original Message-----
> From: Stephan Preibisch [mailto:[hidden email]]
> Sent: Tuesday, 16 November 2010 2:03 p.m.
> To: 'ImageJ Interest Group'
> Cc: Jacqui Ross
> Subject: RE: FIJI 2D stitching in a macro
>
> Hi,
>
> you should be able to record a macro that stores what allowed you to
> merge it for one timepoint. In the ideal case you simple make a loop
> over the 1000 images and it should be fine. At which point are you
> stuck?
>
> Nice greetings,
> Stephan
>
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf

Of

> > Jacqui Ross
> > Sent: Montag, 15. November 2010 21:53
> > To: [hidden email]
> > Subject: FIJI 2D stitching in a macro
> >
> > Dear All,
> >
> > One of our users has acquired time-lapse data on a Nikon BioStation
> > that she now wants to merge into a movie. She has acquired 3 images
> at
> > each time point, which can be merged together nicely using the 2D
> > Stitch plugin.
> >
> > However, there are over 1000 sets of images ("top", "middle" and
> > "bottom") to be merged.
> >
> > Is anyone able to let me know how I can put this into a macro? We
> have
> > 3
> > data sets of tiff files sequentially named in 3 individual folders,
> > top, middle and bottom. The tiling is not straightforward in that it
> > is
> like
> > a zigzag rather than a rectangle. However, the 2D plugin did merge
> the
> > 3
> > images very well so if we can automate the procedure and obtain the
> > merged tiff files for each time point, we can then easily build the
> > AVI.
> >
> > I have looked at the batch processing options but I haven't figured
> out
> > how to select the correct images.
> >
> > Thanks in advance for any assistance.
> >
> > Kind regards,
> >
> > Jacqui
> >
> > Jacqueline Ross
> >
> > Biomedical Imaging Microscopist
> > Biomedical Imaging Research Unit
> > School of Medical Sciences
> > Faculty of Medical & Health Sciences
> > The University of Auckland
> > Private Bag 92019
> > Auckland, NEW ZEALAND
> >
> > Tel: [phone] Ext 87438
> > Fax: [phone]
> >
> > http://www.fmhs.auckland.ac.nz/sms/biru/