Analyze Plugin

[Ekene Avery]

Has anyone been able to view Analyze files in an ImageJ applet?
If so, please let me know the procedure that you used to accomplish this
because it seems to be more difficult than just adding the
Analyze_Reader/Writer class and the HandleExtraFileTypes class.

Thanks

Ekene Avery
UPENN - Center for Functional Neuroimaging

[Daniel Mauch]

Hi All

I am doing my PhD in medical image processing at the TU- Munich in Germany.
I am searching for people who have images that cannot be analysed.

If you know somebody, it would be very helpful if you could send me the
contact information's or the images.

With kind regards
Daniel Mauch
[hidden email]

[Burger Wilhelm]

Could you be more explicit on what you mean by "cannot be analysed"?

W. Burger
www.imagingbook.com


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Daniel Mauch
Sent: Wednesday, February 08, 2006 9:29 PM
To: [hidden email]
Subject: Images that can not be Analysed

Hi All

I am doing my PhD in medical image processing at the TU- Munich in
Germany.
I am searching for people who have images that cannot be analysed.

If you know somebody, it would be very helpful if you could send me the
contact information's or the images.

With kind regards
Daniel Mauch
[hidden email]

[Albert Cardona]

If you mean images that cannot be properly segmented, or that have devilish
color gradients that make it very difficult to count particles, or to measure
intensity, other than by the human eye, I can send you a bunch. Are you
intending to tackle the problem in some way?

Albert

[Monique Vasseur]

I have DIC neurone images with whom I can not get a good threshold to measure automatically the length of the dendrites.

Here is the small image problem example: a DIC transmitted light image taken on a fluorescence microscope.  Very often, it is easy to do threshold on fluorescence images (bright signal over a black background and no "edge shadowing") but on a DIC (differential Interference Contrast also called Nomarski) image, the "3D look" of the image mimics a kind of side-illumination that makes thin structures visible (dendrites in our case) but makes it very hard to threshold to get automatic measurements on it.  We need to measure the length of curved prolongations (dendrites) which don't have the same "edge shadowing" all along the way - so then the threshold never gives good result: we are always on the side of the track and/or the track is not always continuous - so we have to do everything manually with the mouse which is not easy.

So if someone can overpass this threshold problem of DIC images it would permit us to automate the skeleton detection and the length measurement of the dendrites on the DIC image; and then our final goal measure the distance run by dim fluorescent points along that dendrite taking account of the path followed (not straight distance between beginning and arrival, but distance following the curved path from nucleus to the loci on the dendrite).

If this kind of image interests you, I will send you some.

Many thanks in advance.

Monique Vasseur
Microscopie et imagerie
Département de biochimie
Université de Montréal
tél. [phone] poste 5148

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de Daniel Mauch
Envoyé : 8 février 2006 15:29
À : [hidden email]
Objet : Images that can not be Analysed

Hi All

I am doing my PhD in medical image processing at the TU- Munich in Germany.
I am searching for people who have images that cannot be analysed.

If you know somebody, it would be very helpful if you could send me the
contact information's or the images.

With kind regards
Daniel Mauch
[hidden email]

[Michael Cammer]

I have put a 16 bit raw data stack of cultured mammalian cell time lapse at
http://cammer.net/temp/20031208-primary.tif

We would like to have each cell precision traced at each time point so that
1.) morphometrics may be performed and 2.) the tracing may be used as a
mask for analysis of fluorescence data of the same cells over time.  N.b.
the very thin membrane protruding and retracting; this needs to be traced
properly.

Thanks for trying this!

-Michael

At 11:34 AM 02/09/06 +0100, you wrote:
>If you mean images that cannot be properly segmented, or that have devilish
>color gradients that make it very difficult to count particles, or to measure
>intensity, other than by the human eye, I can send you a bunch. Are you
>intending to tackle the problem in some way?
>
>Albert

____________________________________________________________________________
Michael Cammer   Analytical Imaging Facility   Albert Einstein Coll. of Med.
Jack & Pearl Resnick Campus      1300 Morris Park Ave.     Bronx, NY  10461
[phone]       Fax:  [phone]      URL:  http://www.aecom.yu.edu/aif/
   **This electronic transmission contains information that is privileged.**

[Michael Cammer]

Could ImageJ be used to confirm these results?
http://www.nytimes.com/2006/02/09/arts/design/09poll.html?ex=1140152400&en=bea48bef734ae62f&ei=5070&emc=eta1
and
http://www.nature.com/news/2006/060206/full/439648a.html

____________________________________________________________________________
Michael Cammer   Analytical Imaging Facility   Albert Einstein Coll. of Med.
Jack & Pearl Resnick Campus      1300 Morris Park Ave.     Bronx, NY  10461
[phone]       Fax:  [phone]      URL:  http://www.aecom.yu.edu/aif/
   **This electronic transmission contains information that is privileged.**

[H. Gluender]

>Could ImageJ be used to confirm these results?
>http://www.nytimes.com/2006/02/09/arts/design/09poll.html?ex=1140152400&en=bea48bef734ae62f&ei=5070&emc=eta1
>and
>http://www.nature.com/news/2006/060206/full/439648a.html
>
>____________________________________________________________________________
>Michael Cammer   Analytical Imaging Facility   Albert Einstein Coll. of Med.
>Jack & Pearl Resnick Campus      1300 Morris Park Ave.     Bronx, NY  10461
>[phone]       Fax:  [phone]      URL:  http://www.aecom.yu.edu/aif/
>   **This electronic transmission contains information that is privileged.**

Michael,

if you're really with the above facility, I'm sure you will know what
software can do. It does what programmers have put into it. Go ahead
and use ImageJ to assist you in fractal image analysis but be aware
that there are hundreds of ways of doing it...

Best
--


                   Herbie

          ------------------------

          <http://www.gluender.de>

[Martin du Saire]

Following up on this...Is there a measure of whether or not as set of
images can be analyzed automatically?

M

At 02:29 PM 2/8/2006, you wrote:

>Hi All
>
>I am doing my PhD in medical image processing at the TU- Munich in Germany.
>I am searching for people who have images that cannot be analysed.
>
>If you know somebody, it would be very helpful if you could send me the
>contact information's or the images.
>
>With kind regards
>Daniel Mauch
>[hidden email]

[Daniel Mauch]

Hello

I mean images which can be easily be segmented by humans but nearly not by
the PC

Greetings
Daniel

-----Ursprüngliche Nachricht-----
Von: [hidden email] [mailto:[hidden email]] Im Auftrag
von Albert Cardona
Gesendet: Donnerstag, 9. Februar 2006 11:34
An: [hidden email]
Betreff: Re: Images that can not be Analysed

If you mean images that cannot be properly segmented, or that have devilish
color gradients that make it very difficult to count particles, or to
measure
intensity, other than by the human eye, I can send you a bunch. Are you
intending to tackle the problem in some way?

Albert