Matlab and ImageJ compatibility

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Matlab and ImageJ compatibility

Pang, Zhengyu (GE Global Research)
Dear all,

I got some images from the folks using Matlab image processing tool box.
When matlab saved TIFF file, the default is compressed TIFF, and this
form could not be read by ImageJ. Did everyone have the similar
situation?

Is there a plugin that can read Matlab compressed TIFF image?

Thanks!

Zhengyu
> g Global Research Center
>
> ______________________________________________________________________
>
>           Zhengyu Pang, Ph.D.
                        Bioanalytics and Protein Science Laboratory
                        Biosciences Global Technology Organization
> One Research Circle, K1 5B37A
> Niskayuna, NY12309
> * [hidden email]
> *(518) 387-4015
>
>
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Re: Matlab and ImageJ compatibility

Jeffrey B. Woodward
I run into this issue *all* the time with the folks that I collaborate
with. I use the sourceforge imageio plugin:

http://ij-plugins.sourceforge.net/plugins/imageio/

Best of luck,

-Woody


Pang, Zhengyu (GE, Research) wrote:

> Dear all,
>
> I got some images from the folks using Matlab image processing tool box.
> When matlab saved TIFF file, the default is compressed TIFF, and this
> form could not be read by ImageJ. Did everyone have the similar
> situation?
>
> Is there a plugin that can read Matlab compressed TIFF image?
>
> Thanks!
>
> Zhengyu
>  
>> g Global Research Center
>>
>> ______________________________________________________________________
>>
>>           Zhengyu Pang, Ph.D.
>>    
> Bioanalytics and Protein Science Laboratory
> Biosciences Global Technology Organization
>  
>> One Research Circle, K1 5B37A
>> Niskayuna, NY12309
>> * [hidden email]
>> *(518) 387-4015
>>
>>
>>    
>
>
>  
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Re: Matlab and ImageJ compatibility

Wayne Rasband
In reply to this post by Pang, Zhengyu (GE Global Research)
On Oct 17, 2008, at 11:51 AM, Pang, Zhengyu (GE, Research) wrote:

> Dear all,
>
> I got some images from the folks using Matlab image processing tool
> box.
> When matlab saved TIFF file, the default is compressed TIFF, and this
> form could not be read by ImageJ. Did everyone have the similar
> situation?
>
> Is there a plugin that can read Matlab compressed TIFF image?

The Bio-Formats plugin opens the PackBits compressed TIFFs created by
Matlab. With the latest Bio-Formats you can open TIFFs by dragging and
dropping them on the LOCI shortcuts window (Plugins>LOCI>LOCI Plugins
Shortcut Window).

-wayne
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Re: Matlab and ImageJ compatibility

Wayne Rasband
In reply to this post by Pang, Zhengyu (GE Global Research)
> I got some images from the folks using Matlab image processing tool
> box.
> When matlab saved TIFF file, the default is compressed TIFF, and this
> form could not be read by ImageJ. Did everyone have the similar
> situation?
>
> Is there a plugin that can read Matlab compressed TIFF image?

ImageJ 1.41n does not need a plugin to open PackBits compressed TIFF
images created by Matlab.

-wayne
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Re: Matlab and ImageJ compatibility

Jeffrey B. Woodward
Wayne Rasband wrote:

>> I got some images from the folks using Matlab image processing tool box.
>> When matlab saved TIFF file, the default is compressed TIFF, and this
>> form could not be read by ImageJ. Did everyone have the similar
>> situation?
>>
>> Is there a plugin that can read Matlab compressed TIFF image?
>
> ImageJ 1.41n does not need a plugin to open PackBits compressed TIFF
> images created by Matlab.
>
> -wayne
>
>

That's great news...thanks Wayne!

-Woody
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Angle tool - problems.

Gareth Martin
Dear All,
             Hello. I'm new to the list but have used ImageJ for a while
now, mainly on geomorphic data, and  have found it to be an excellent
programme. I've currently begun to use ImageJ to analyse my archery ends
to obtain the distance from the centre of the target face and angle from
the vertical of the arrows I have shot. I use the measuring tools for
this, namely the Angle tool and Straight Line Selection tool. However
I've noticed that the angle tool does not directly measure a full 360
degrees but measures up to 180 degrees and then decreases again. I
understand this is surmountable with some simple mathematics but this
slows down my data entry and analysis somewhat! I've searched the forum
and the ImageJ documentation but am no further to finding a solution.
Could anyone offer any solutions to my problem? Thanks very much in
advance for any help.

Best wishes,
Gareth.
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Re: Angle tool - problems.

Gareth Martin
Dear All,
            Hello. I'm new to the list but have used ImageJ for a while
now, mainly on geomorphic data, and  have found it to be an excellent
programme. I've currently begun to use ImageJ to analyse my archery ends
to obtain the distance from the centre of the target face and angle from
the vertical of the arrows I have shot. I use the measuring tools for
this, namely the Angle tool and Straight Line Selection tool but have
noticed that both tools do not measure from 0 to 360 degrees. I
understand this is surmountable with some simple mathematics but this
slows down my data entry and analysis somewhat! I've searched the forum
and the ImageJ documentation but am no further to finding a solution.
Could anyone offer any solutions to my problem? Thanks very much in
advance for any help.

Best wishes,
Gareth.
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Re: Angle tool - problems.

Michael Schmid
Hi Gareth,

the Angle Tool does not have two different symbols for the two ends  
of the angle, so one cannot see which end was clicked first. Thus, I  
think it would be confusing to get, e.g., either "+60°" or  
"300°" (=-60°) from angle tool selections that look absolutely  
identical.

If you know that you always click on one type of feature first, then  
on the vertex and then on the other feature, you could use a simple  
macro that gives the angle with a sign:

if (selectionType() !=8) exit ("No Angle Selection");
getSelectionCoordinates(x, y);
angle=57.2957795131*(atan2(y[0]-y[1],x[0]-x[1])-atan2(y[2]-y[1],x[2]-x
[1]));
angle=(angle+360)%360;
print (angle);

Michael
________________________________________________________________

On 19 Oct 2008, at 23:53, Gareth Martin wrote:

> Dear All,
>            Hello. I'm new to the list but have used ImageJ for a  
> while now, mainly on geomorphic data, and  have found it to be an  
> excellent programme. I've currently begun to use ImageJ to analyse  
> my archery ends to obtain the distance from the centre of the  
> target face and angle from the vertical of the arrows I have shot.  
> I use the measuring tools for this, namely the Angle tool and  
> Straight Line Selection tool but have noticed that both tools do  
> not measure from 0 to 360 degrees. I understand this is  
> surmountable with some simple mathematics but this slows down my  
> data entry and analysis somewhat! I've searched the forum and the  
> ImageJ documentation but am no further to finding a solution. Could  
> anyone offer any solutions to my problem? Thanks very much in  
> advance for any help.
>
> Best wishes,
> Gareth.