opening stacks

[Morgiane Richard]

Dear ImagJer,
 
I want to import a sequence of tiff images, which names start with a string and then a number, that is to say:
"string1.tiff", "string2.tiff", etc...
The problem is ImageJ import the files as a sequence, but in the following order: "string1.tiff", "string10.tiff"...."string19.tiff", "string2.tiff", etc...
I dont know how to impose the order of teh sequence. I have tried to put an increment of 11 in the dialog box and 99 images as the total number of images to be opened, but then only the first 9 images are opened.
 
Thank you,
 
Morgiane
 

[Carl Sebeny]

Try re-naming your files as follows:

  string01.tiff, string02.tiff, ..., string09.tiff, string10.tiff, ...

________________________________

Carl Sebeny
Imaging Scientist
Applied Vision Company, LLC

330.926.2222 phone
330.926.2210 direct
330.926.2250 fax
www.appliedvision.com

 

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
M.Richard
Sent: Wednesday, October 19, 2005 7:48 AM
To: [hidden email]
Subject: opening stacks

Dear ImagJer,
 
I want to import a sequence of tiff images, which names start with a
string and then a number, that is to say:
"string1.tiff", "string2.tiff", etc...
The problem is ImageJ import the files as a sequence, but in the
following order: "string1.tiff", "string10.tiff"...."string19.tiff",
"string2.tiff", etc...
I dont know how to impose the order of teh sequence. I have tried to put
an increment of 11 in the dialog box and 99 images as the total number
of images to be opened, but then only the first 9 images are opened.
 
Thank you,
 
Morgiane
 

[Noel BONNET]

On Wed, 19 Oct 2005 12:48:20 +0100, M.Richard <[hidden email]> wrote:

>Dear ImagJer,
>
>I want to import a sequence of tiff images, which names start with a string
and then a number, that is to say:
>"string1.tiff", "string2.tiff", etc...
>The problem is ImageJ import the files as a sequence, but in the following
order: "string1.tiff", "string10.tiff"...."string19.tiff", "string2.tiff",
etc...
>I dont know how to impose the order of teh sequence. I have tried to put an
increment of 11 in the dialog box and 99 images as the total number of
images to be opened, but then only the first 9 images are opened.
>
>Thank you,
>
>Morgiane
>
>========================================================================

Isn't it possible to have your images named "string001.tiff",
"string002.tiff", ... "string011.tiff", etc...
This option is available with most image acquisition softwares.

Good luck.

Noel

[Bertram Becher]

A good tool for batch conversion and renaming is the freeware IrfanView.

Greetings

Bertram Becher
______________________________________________________________________
XXL-Speicher, PC-Virenschutz, Spartarife & mehr: Nur im WEB.DE Club!
Jetzt gratis testen! http://freemail.web.de/home/landingpad/?mc=021130

[Joachim Walter]

Morgiane,

I think you need "XP-style" file ordering, i.e. a consecutive sequence
of digits is treated as numbers and the files are sorted by these
numbers. Actually, on my PC running Windows XP a file sequence like you
describe opens correctly in ImageJ.
You might try the HyperVolume Opener, which is one of the plugins in the
Image5D plugin collection, available from the ImageJ website. I
explicitly implemented this type of file sorting in the plugin, so it
should also work on other operating systems.

Joachim

M.Richard schrieb:

> Dear ImagJer,
>
> I want to import a sequence of tiff images, which names start with a
> string and then a number, that is to say: "string1.tiff",
> "string2.tiff", etc... The problem is ImageJ import the files as a
> sequence, but in the following order: "string1.tiff",
> "string10.tiff"...."string19.tiff", "string2.tiff", etc... I dont
> know how to impose the order of teh sequence. I have tried to put an
> increment of 11 in the dialog box and 99 images as the total number
> of images to be opened, but then only the first 9 images are opened.
>
> Thank you,
>
> Morgiane
>
>

--
-----------------------------------------------
Dr. Joachim Walter

TILL I.D. GmbH
c\o BioImaging Zentrum
Großhaderner Str. 2
D-82152 Martinsried

Tel.: [phone]
Fax:  [phone]

[hidden email]

[Richard Murray-3]

You'll either need to rename your files numerically or get the 'xp-style'
image j

> Morgiane,
>
> I think you need "XP-style" file ordering, i.e. a consecutive sequence
> of digits is treated as numbers and the files are sorted by these
> numbers. Actually, on my PC running Windows XP a file sequence like you
> describe opens correctly in ImageJ.
> You might try the HyperVolume Opener, which is one of the plugins in the
> Image5D plugin collection, available from the ImageJ website. I
> explicitly implemented this type of file sorting in the plugin, so it
> should also work on other operating systems.
>
> Joachim
>
> M.Richard schrieb:
>> Dear ImagJer,
>>
>> I want to import a sequence of tiff images, which names start with a
>> string and then a number, that is to say: "string1.tiff",
>> "string2.tiff", etc... The problem is ImageJ import the files as a
>> sequence, but in the following order: "string1.tiff",
>> "string10.tiff"...."string19.tiff", "string2.tiff", etc... I dont
>> know how to impose the order of teh sequence. I have tried to put an
>> increment of 11 in the dialog box and 99 images as the total number
>> of images to be opened, but then only the first 9 images are opened.
>>
>> Thank you,
>>
>> Morgiane
>>
>>
>
>
> --
> -----------------------------------------------
> Dr. Joachim Walter
>
> TILL I.D. GmbH
> c\o BioImaging Zentrum
> Großhaderner Str. 2
> D-82152 Martinsried
>
> Tel.: [phone]
> Fax:  [phone]
>
> [hidden email]
>

--
Richard Murray BSc.
Nanoscale Biophotonics Research Group,
NCBES, Orbsen Biulding,
NUI Galway
Galway,
Ireland
email: [hidden email]
phone:[phone]

[Smellie, Andrew]

Is it possible to write macros that can drive plugins?

I am recording a macro that invokes a plug in (in this case the ColorHistogram
plugin). I can invoke the macro to generate three histograms of rgb values,
but need to issue a command to the plugin to export the histogram to a text file
Is this possible?

The actual problem I am trying to solve is to generate histograms of rbg values
for an image autmatically from a command line macro. How might I achieve this?

Thanks

Andrew

Andrew Smellie, B.A., D.Phil. (Oxon)
Senior Investigator II
Arqule Inc.
19 Presidential Way,
Woburn, MA 01801
[hidden email]
Phone: [phone]

[Albert Cardona]

For my own amusement I've written a plugin that opens a sequence of
image files into a stack.

http://www.pensament.net/java/other_plugins.html

 From the website:
- Open sequentially as stack: A plugin to open a sequence of images
following the natural order, i.e. IMG_11.tif will go after IMG_6.tif.
After the user selects an image file, the non-numeric characters of the
name are used to filter files from that directory, thus other sequences
of image files and/or other non-image files can coexist in the same
directory without problems. The extension of the files to open does not
have to be the same as that of the user-selected image file.
Images that have different width & height than that of the first image
in the sequence will not be opened.

Albert