imageJ use?

[Blake Elder]

Hi

I'm an marine science undergraduate with roughly 600 pictures of coral samples that need to be quantified for bleaching. I was wondering if there is a process in ImageJ that I could use to uniquely identify the color of each sample in relation to all of the other pictures. This value would have to be something I can use to determine if bleaching was worse in some samples compared to others. All pictures were taken in a standardized view and lighting but I may also need to correct for slight glares, shading, etc. from picture to picture in the analysis.

I'm very new to the software and appreciate any help offered.

Anyone have any ideas?

Thanks
Blake

[Cammer, Michael]

It would help if all the pictures were taken with a standard color chart in them, such as a Macbeth chart. Or is there some other feature in the photos that is known to remain unchanged so that it may be used as a reference?  On the other hand, if they were really taken under standard conditions, why not simply measure the intensities of each coral and see if the errors fall out when averages are done?

I had a case a few years ago where someone came to me with about a thousand poorly lit and compressed jpeg files that they wanted to quantify.  I had to ask, why didn't you ask about this BEFORE you shot the pictures?  Or three years ago when you wrote the grant application?  I know that we often come up with nifty ideas for analysis after we have the data, but in a case like this the problem must have been defined in advance.

Ok, enough preaching.  Now maybe someone could practically help Blake...

________________________________________________________
Michael Cammer, Assistant Research Scientist Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Blake Elder
Sent: Wednesday, February 08, 2012 10:05 PM
To: [hidden email]
Subject: imageJ use?

Hi

I'm an marine science undergraduate with roughly 600 pictures of coral samples that need to be quantified for bleaching. I was wondering if there is a process in ImageJ that I could use to uniquely identify the color of each sample in relation to all of the other pictures. This value would have to be something I can use to determine if bleaching was worse in some samples compared to others. All pictures were taken in a standardized view and lighting but I may also need to correct for slight glares, shading, etc. from picture to picture in the analysis.

I'm very new to the software and appreciate any help offered.

Anyone have any ideas?

Thanks
Blake

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

[Anderson, Charles (DNR)]

If Blake were to attach a couple small images, with a description of how he thinks those would be scored/interpreted, perhaps someone could offer suggestions. Without them, many of us are just guessing at what he means by color, bleaching, shade, glare, or quantify.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Cammer, Michael
Sent: Thursday, February 09, 2012 12:47 PM
To: [hidden email]
Subject: Re: imageJ use?

It would help if all the pictures were taken with a standard color chart in them, such as a Macbeth chart. Or is there some other feature in the photos that is known to remain unchanged so that it may be used as a reference?  On the other hand, if they were really taken under standard conditions, why not simply measure the intensities of each coral and see if the errors fall out when averages are done?

I had a case a few years ago where someone came to me with about a thousand poorly lit and compressed jpeg files that they wanted to quantify.  I had to ask, why didn't you ask about this BEFORE you shot the pictures?  Or three years ago when you wrote the grant application?  I know that we often come up with nifty ideas for analysis after we have the data, but in a case like this the problem must have been defined in advance.

Ok, enough preaching.  Now maybe someone could practically help Blake...

________________________________________________________
Michael Cammer, Assistant Research Scientist Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Blake Elder
Sent: Wednesday, February 08, 2012 10:05 PM
To: [hidden email]
Subject: imageJ use?

Hi

I'm an marine science undergraduate with roughly 600 pictures of coral samples that need to be quantified for bleaching. I was wondering if there is a process in ImageJ that I could use to uniquely identify the color of each sample in relation to all of the other pictures. This value would have to be something I can use to determine if bleaching was worse in some samples compared to others. All pictures were taken in a standardized view and lighting but I may also need to correct for slight glares, shading, etc. from picture to picture in the analysis.

I'm very new to the software and appreciate any help offered.

Anyone have any ideas?

Thanks
Blake

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

[Paul Grimm-2]

Hi
I am scratching my head. I have a piece of code directly copied from an email by Wayne in 2010. It runs great as a macro at regular speeds (Debug, then Run)
But if I step through it, one command is not carried out and the macro fails.

The command that works at full speed but not when stepping through is
   selectWindow("Unsmoothed");
   IJ.renameResults("Results");

when I step through, the "Unsmoothed" results table does not get renamed,
when I run this at regular speed, or in batchmode, or if I execute a chunk of the code, then "run to insertion point" and set my cursor 5 or 6 lines down below that point,  whatever, it works fine. I removed all the batchmode commands and that made no difference. I then tried to put setBatchMode(true) and (false) commands around the offending lines of code and that worked sometimes.

WHY?

Here is the whole code.

>
> On Jun 7, 2010, at 2:21 AM, Aryeh Weiss wrote:
>
> > Rasband, Wayne (NIH/NIMH) [E] wrote:
> >>> Dear list,
> >>>
> >>> Is it possible to create two different result tables in the same macro?
> >>> For example I'm working with two stacks, applying some measurements
> >>> on the nuclei and then on the fluorescent particles in every nucleus.
> >>> So I need one result table for the nuclei and the other for the included
> >>> particles, because every one has its own measurements.
> >>> Is it possible in imagej?
> >>
> >> You can create multiple result tables in the 1.44c4 daily build by using the new "Rename" command, available in the File menu of Results windows. Here is an example macro that uses the corresponding IJ.renameResults() macro function to create two result tables.
> >>
> >>   run("Blobs (25K)");
> >>   setAutoThreshold("Default");
> >>   run("Analyze Particles...", "display clear");
> >>   IJ.renameResults("Unsmoothed");
> >>   run("Gaussian Blur...", "sigma=2");
> >>   setAutoThreshold("Default");
> >>   run("Analyze Particles...", "display clear");
> >>   IJ.renameResults("Smoothed");
> >>
> >> -wayne
> >>
> >
> > This is great!
> >
> > Can the functions that access the results table (getResults, etc) select
> > which result table to use?
> ... [show rest of quote]
>
> Macro functions like getResults() only work with the primary results table so you have to rename the table you want to access to "Results". I have included an example. Plugins and scripts can get a reference to the underlining ResultsTable object and use the rt.getValue() method.
>
> -wayne
>
>    setBatchMode(true);
>    run("Blobs (25K)");
>    run("Set Measurements...", "area mean min decimal=2");
>    setAutoThreshold("Default");
>    run("Analyze Particles...", "display clear add");
>    IJ.renameResults("Unsmoothed");
>    run("Gaussian Blur...", "sigma=2");
>    n = roiManager("count");
>    for (i=0; i<n; i++) {
>        roiManager("select", i)
>        run("Measure");
>    }
>    mean1 = newArray(n);
>    mean2 = newArray(n);
>    IJ.renameResults("Smoothed");
>    selectWindow("Unsmoothed");
>    IJ.renameResults("Results");
>    for (i=0; i<n; i++)
>        mean1[i] = getResult("Mean", i);
>    selectWindow("Smoothed");
>    IJ.renameResults("Results");
>    for (i=0; i<n; i++)
>        mean2[i] = getResult("Mean", i);
>    run("Clear Results");
>    for (i=0; i<n; i++) {
>        setResult("Mean1", i, mean1[i]);
>        setResult("Mean2", i, mean2[i]);
>        setResult("%Difference", i, (mean1[i]-mean2[i])*100/mean1[i]);
>    }
>    updateResults();
>

--


Paul C. Grimm
Professor of Pediatrics
Dept of Pediatric Nephrology
Lucile Packard Children's Hospital
Stanford University School of Medicine
G306, MC 5208
300 Pasteur Drive
Stanford, CA 94305-5208
USA

phone   [phone]
fax       [phone]


Never argue with a fool. He'll only drag you down to his level and beat you with experience.’




On Feb 10, 2012, at 1:30 PM, Anderson, Charles (DNR) wrote:

> If Blake were to attach a couple small images, with a description of how he thinks those would be scored/interpreted, perhaps someone could offer suggestions. Without them, many of us are just guessing at what he means by color, bleaching, shade, glare, or quantify.
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Cammer, Michael
> Sent: Thursday, February 09, 2012 12:47 PM
> To: [hidden email]
> Subject: Re: imageJ use?
>
> It would help if all the pictures were taken with a standard color chart in them, such as a Macbeth chart. Or is there some other feature in the photos that is known to remain unchanged so that it may be used as a reference?  On the other hand, if they were really taken under standard conditions, why not simply measure the intensities of each coral and see if the errors fall out when averages are done?
>
> I had a case a few years ago where someone came to me with about a thousand poorly lit and compressed jpeg files that they wanted to quantify.  I had to ask, why didn't you ask about this BEFORE you shot the pictures?  Or three years ago when you wrote the grant application?  I know that we often come up with nifty ideas for analysis after we have the data, but in a case like this the problem must have been defined in advance.
>
> Ok, enough preaching.  Now maybe someone could practically help Blake...
>
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Blake Elder
> Sent: Wednesday, February 08, 2012 10:05 PM
> To: [hidden email]
> Subject: imageJ use?
>
> Hi
>
> I'm an marine science undergraduate with roughly 600 pictures of coral samples that need to be quantified for bleaching. I was wondering if there is a process in ImageJ that I could use to uniquely identify the color of each sample in relation to all of the other pictures. This value would have to be something I can use to determine if bleaching was worse in some samples compared to others. All pictures were taken in a standardized view and lighting but I may also need to correct for slight glares, shading, etc. from picture to picture in the analysis.
>
> I'm very new to the software and appreciate any help offered.
>
> Anyone have any ideas?
>
> Thanks
> Blake
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
> =================================

[Rasband, Wayne (NIH/NIMH) [E]]

On Feb 10, 2012, at 7:04 PM, Paul Grimm wrote:

> Hi
> I am scratching my head. I have a piece of code directly copied from an email by Wayne in 2010. It runs great as a macro at regular speeds (Debug, then Run)
> But if I step through it, one command is not carried out and the macro fails.
>
> The command that works at full speed but not when stepping through is
>   selectWindow("Unsmoothed");
>   IJ.renameResults("Results");

The selectWindow() macro function does not work with non-image windows when single stepping through a macro using the debugger. You can work around this problem by upgrading to the ImageJ 1.46g daily build and changing

    selectWindow("Unsmoothed");
    IJ.renameResults("Results");

to

    IJ.renameResults("Unsmoothed", "Results");

Here is an updated version of the example that uses the new two argument version of IJ.renameResults().

  setBatchMode(true);
  run("Blobs (25K)");
  run("Set Measurements...", "area mean min decimal=2");
  setAutoThreshold("Default");
  run("Analyze Particles...", "display clear add");
  IJ.renameResults("Results", "Unsmoothed");
  run("Gaussian Blur...", "sigma=2");
  n = roiManager("count");
  for (i=0; i<n; i++) {
      roiManager("select", i)
      run("Measure");
  }
  mean1 = newArray(n);
  mean2 = newArray(n);
  IJ.renameResults("Results", "Smoothed");
  IJ.renameResults("Unsmoothed", "Results");
  for (i=0; i<n; i++)
      mean1[i] = getResult("Mean", i);
  IJ.renameResults("Smoothed", "Results");
  for (i=0; i<n; i++)
      mean2[i] = getResult("Mean", i);
  run("Clear Results");
  for (i=0; i<n; i++) {
      setResult("Mean1", i, mean1[i]);
      setResult("Mean2", i, mean2[i]);
      setResult("%Difference", i, (mean1[i]-mean2[i])*100/mean1[i]);
  }
  updateResults();


-wayne

> when I step through, the "Unsmoothed" results table does not get renamed,
> when I run this at regular speed, or in batchmode, or if I execute a chunk of the code, then "run to insertion point" and set my cursor 5 or 6 lines down below that point,  whatever, it works fine. I removed all the batchmode commands and that made no difference. I then tried to put setBatchMode(true) and (false) commands around the offending lines of code and that worked sometimes.
>
> WHY?
>
> Here is the whole code.
>
>>
>> On Jun 7, 2010, at 2:21 AM, Aryeh Weiss wrote:
>>
>>> Rasband, Wayne (NIH/NIMH) [E] wrote:
>>>>> Dear list,
>>>>>
>>>>> Is it possible to create two different result tables in the same macro?
>>>>> For example I'm working with two stacks, applying some measurements
>>>>> on the nuclei and then on the fluorescent particles in every nucleus.
>>>>> So I need one result table for the nuclei and the other for the included
>>>>> particles, because every one has its own measurements.
>>>>> Is it possible in imagej?
>>>>
>>>> You can create multiple result tables in the 1.44c4 daily build by using the new "Rename" command, available in the File menu of Results windows. Here is an example macro that uses the corresponding IJ.renameResults() macro function to create two result tables.
>>>>
>>>>  run("Blobs (25K)");
>>>>  setAutoThreshold("Default");
>>>>  run("Analyze Particles...", "display clear");
>>>>  IJ.renameResults("Unsmoothed");
>>>>  run("Gaussian Blur...", "sigma=2");
>>>>  setAutoThreshold("Default");
>>>>  run("Analyze Particles...", "display clear");
>>>>  IJ.renameResults("Smoothed");
>>>>
>>>> -wayne
>>>>
>>>
>>> This is great!
>>>
>>> Can the functions that access the results table (getResults, etc) select
>>> which result table to use?
>> ... [show rest of quote]
>>
>> Macro functions like getResults() only work with the primary results table so you have to rename the table you want to access to "Results". I have included an example. Plugins and scripts can get a reference to the underlining ResultsTable object and use the rt.getValue() method.
>>
>> -wayne
>>
>>   setBatchMode(true);
>>   run("Blobs (25K)");
>>   run("Set Measurements...", "area mean min decimal=2");
>>   setAutoThreshold("Default");
>>   run("Analyze Particles...", "display clear add");
>>   IJ.renameResults("Unsmoothed");
>>   run("Gaussian Blur...", "sigma=2");
>>   n = roiManager("count");
>>   for (i=0; i<n; i++) {
>>       roiManager("select", i)
>>       run("Measure");
>>   }
>>   mean1 = newArray(n);
>>   mean2 = newArray(n);
>>   IJ.renameResults("Smoothed");
>>   selectWindow("Unsmoothed");
>>   IJ.renameResults("Results");
>>   for (i=0; i<n; i++)
>>       mean1[i] = getResult("Mean", i);
>>   selectWindow("Smoothed");
>>   IJ.renameResults("Results");
>>   for (i=0; i<n; i++)
>>       mean2[i] = getResult("Mean", i);
>>   run("Clear Results");
>>   for (i=0; i<n; i++) {
>>       setResult("Mean1", i, mean1[i]);
>>       setResult("Mean2", i, mean2[i]);
>>       setResult("%Difference", i, (mean1[i]-mean2[i])*100/mean1[i]);
>>   }
>>   updateResults();
>>
> --
>
>
> Paul C. Grimm
> Professor of Pediatrics
> Dept of Pediatric Nephrology
> Lucile Packard Children's Hospital
> Stanford University School of Medicine
> G306, MC 5208
> 300 Pasteur Drive
> Stanford, CA 94305-5208
> USA
>
> phone   [phone]
> fax       [phone]
>
>
> Never argue with a fool. He'll only drag you down to his level and beat you with experience.’
>
>
>
>
> On Feb 10, 2012, at 1:30 PM, Anderson, Charles (DNR) wrote:
>
>> If Blake were to attach a couple small images, with a description of how he thinks those would be scored/interpreted, perhaps someone could offer suggestions. Without them, many of us are just guessing at what he means by color, bleaching, shade, glare, or quantify.
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Cammer, Michael
>> Sent: Thursday, February 09, 2012 12:47 PM
>> To: [hidden email]
>> Subject: Re: imageJ use?
>>
>> It would help if all the pictures were taken with a standard color chart in them, such as a Macbeth chart. Or is there some other feature in the photos that is known to remain unchanged so that it may be used as a reference?  On the other hand, if they were really taken under standard conditions, why not simply measure the intensities of each coral and see if the errors fall out when averages are done?
>>
>> I had a case a few years ago where someone came to me with about a thousand poorly lit and compressed jpeg files that they wanted to quantify.  I had to ask, why didn't you ask about this BEFORE you shot the pictures?  Or three years ago when you wrote the grant application?  I know that we often come up with nifty ideas for analysis after we have the data, but in a case like this the problem must have been defined in advance.
>>
>> Ok, enough preaching.  Now maybe someone could practically help Blake...
>>
>> ________________________________________________________
>> Michael Cammer, Assistant Research Scientist Skirball Institute of Biomolecular Medicine
>> Lab: [phone]  Cell: [phone]
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Blake Elder
>> Sent: Wednesday, February 08, 2012 10:05 PM
>> To: [hidden email]
>> Subject: imageJ use?
>>
>> Hi
>>
>> I'm an marine science undergraduate with roughly 600 pictures of coral samples that need to be quantified for bleaching. I was wondering if there is a process in ImageJ that I could use to uniquely identify the color of each sample in relation to all of the other pictures. This value would have to be something I can use to determine if bleaching was worse in some samples compared to others. All pictures were taken in a standardized view and lighting but I may also need to correct for slight glares, shading, etc. from picture to picture in the analysis.
>>
>> I'm very new to the software and appreciate any help offered.
>>
>> Anyone have any ideas?
>>
>> Thanks
>> Blake
>>
>> ------------------------------------------------------------
>> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
>> =================================

[Paul Grimm-2]

thank you Wayne....
Again!
--


Paul C. Grimm
Professor of Pediatrics
Dept of Pediatric Nephrology
Lucile Packard Children's Hospital
Stanford University School of Medicine
G306, MC 5208
300 Pasteur Drive
Stanford, CA 94305-5208
USA
phone   [phone]
fax       [phone]


“The heights by great men reached and kept
Were not obtained by sudden flight,
But they, while their companions slept,
Were toiling upward in the night.”

Henry Wadsworth Longfellow
American poet, educator, linguist (1807 — 1882)




On Feb 11, 2012, at 8:36 AM, Rasband, Wayne (NIH/NIMH) [E] wrote:

> On Feb 10, 2012, at 7:04 PM, Paul Grimm wrote:
>
>> Hi
>> I am scratching my head. I have a piece of code directly copied from an email by Wayne in 2010. It runs great as a macro at regular speeds (Debug, then Run)
>> But if I step through it, one command is not carried out and the macro fails.
>>
>> The command that works at full speed but not when stepping through is
>>  selectWindow("Unsmoothed");
>>  IJ.renameResults("Results");
>
> The selectWindow() macro function does not work with non-image windows when single stepping through a macro using the debugger. You can work around this problem by upgrading to the ImageJ 1.46g daily build and changing
>
>    selectWindow("Unsmoothed");
>    IJ.renameResults("Results");
>
> to
>
>    IJ.renameResults("Unsmoothed", "Results");
>
> Here is an updated version of the example that uses the new two argument version of IJ.renameResults().
>
>  setBatchMode(true);
>  run("Blobs (25K)");
>  run("Set Measurements...", "area mean min decimal=2");
>  setAutoThreshold("Default");
>  run("Analyze Particles...", "display clear add");
>  IJ.renameResults("Results", "Unsmoothed");
>  run("Gaussian Blur...", "sigma=2");
>  n = roiManager("count");
>  for (i=0; i<n; i++) {
>      roiManager("select", i)
>      run("Measure");
>  }
>  mean1 = newArray(n);
>  mean2 = newArray(n);
>  IJ.renameResults("Results", "Smoothed");
>  IJ.renameResults("Unsmoothed", "Results");
>  for (i=0; i<n; i++)
>      mean1[i] = getResult("Mean", i);
>  IJ.renameResults("Smoothed", "Results");
>  for (i=0; i<n; i++)
>      mean2[i] = getResult("Mean", i);
>  run("Clear Results");
>  for (i=0; i<n; i++) {
>      setResult("Mean1", i, mean1[i]);
>      setResult("Mean2", i, mean2[i]);
>      setResult("%Difference", i, (mean1[i]-mean2[i])*100/mean1[i]);
>  }
>  updateResults();
>
>
> -wayne
>
>
>> when I step through, the "Unsmoothed" results table does not get renamed,
>> when I run this at regular speed, or in batchmode, or if I execute a chunk of the code, then "run to insertion point" and set my cursor 5 or 6 lines down below that point,  whatever, it works fine. I removed all the batchmode commands and that made no difference. I then tried to put setBatchMode(true) and (false) commands around the offending lines of code and that worked sometimes.
>>
>> WHY?
>>
>> Here is the whole code.
>>
>>>
>>> On Jun 7, 2010, at 2:21 AM, Aryeh Weiss wrote:
>>>
>>>> Rasband, Wayne (NIH/NIMH) [E] wrote:
>>>>>> Dear list,
>>>>>>
>>>>>> Is it possible to create two different result tables in the same macro?
>>>>>> For example I'm working with two stacks, applying some measurements
>>>>>> on the nuclei and then on the fluorescent particles in every nucleus.
>>>>>> So I need one result table for the nuclei and the other for the included
>>>>>> particles, because every one has its own measurements.
>>>>>> Is it possible in imagej?
>>>>>
>>>>> You can create multiple result tables in the 1.44c4 daily build by using the new "Rename" command, available in the File menu of Results windows. Here is an example macro that uses the corresponding IJ.renameResults() macro function to create two result tables.
>>>>>
>>>>> run("Blobs (25K)");
>>>>> setAutoThreshold("Default");
>>>>> run("Analyze Particles...", "display clear");
>>>>> IJ.renameResults("Unsmoothed");
>>>>> run("Gaussian Blur...", "sigma=2");
>>>>> setAutoThreshold("Default");
>>>>> run("Analyze Particles...", "display clear");
>>>>> IJ.renameResults("Smoothed");
>>>>>
>>>>> -wayne
>>>>>
>>>>
>>>> This is great!
>>>>
>>>> Can the functions that access the results table (getResults, etc) select
>>>> which result table to use?
>>> ... [show rest of quote]
>>>
>>> Macro functions like getResults() only work with the primary results table so you have to rename the table you want to access to "Results". I have included an example. Plugins and scripts can get a reference to the underlining ResultsTable object and use the rt.getValue() method.
>>>
>>> -wayne
>>>
>>>  setBatchMode(true);
>>>  run("Blobs (25K)");
>>>  run("Set Measurements...", "area mean min decimal=2");
>>>  setAutoThreshold("Default");
>>>  run("Analyze Particles...", "display clear add");
>>>  IJ.renameResults("Unsmoothed");
>>>  run("Gaussian Blur...", "sigma=2");
>>>  n = roiManager("count");
>>>  for (i=0; i<n; i++) {
>>>      roiManager("select", i)
>>>      run("Measure");
>>>  }
>>>  mean1 = newArray(n);
>>>  mean2 = newArray(n);
>>>  IJ.renameResults("Smoothed");
>>>  selectWindow("Unsmoothed");
>>>  IJ.renameResults("Results");
>>>  for (i=0; i<n; i++)
>>>      mean1[i] = getResult("Mean", i);
>>>  selectWindow("Smoothed");
>>>  IJ.renameResults("Results");
>>>  for (i=0; i<n; i++)
>>>      mean2[i] = getResult("Mean", i);
>>>  run("Clear Results");
>>>  for (i=0; i<n; i++) {
>>>      setResult("Mean1", i, mean1[i]);
>>>      setResult("Mean2", i, mean2[i]);
>>>      setResult("%Difference", i, (mean1[i]-mean2[i])*100/mean1[i]);
>>>  }
>>>  updateResults();
>>>
>> --
>>
>>
>> Paul C. Grimm
>> Professor of Pediatrics
>> Dept of Pediatric Nephrology
>> Lucile Packard Children's Hospital
>> Stanford University School of Medicine
>> G306, MC 5208
>> 300 Pasteur Drive
>> Stanford, CA 94305-5208
>> USA
>>
>> phone   [phone]
>> fax       [phone]
>>
>>
>> Never argue with a fool. He'll only drag you down to his level and beat you with experience.’
>>
>>
>>
>>
>> On Feb 10, 2012, at 1:30 PM, Anderson, Charles (DNR) wrote:
>>
>>> If Blake were to attach a couple small images, with a description of how he thinks those would be scored/interpreted, perhaps someone could offer suggestions. Without them, many of us are just guessing at what he means by color, bleaching, shade, glare, or quantify.
>>>
>>> -----Original Message-----
>>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Cammer, Michael
>>> Sent: Thursday, February 09, 2012 12:47 PM
>>> To: [hidden email]
>>> Subject: Re: imageJ use?
>>>
>>> It would help if all the pictures were taken with a standard color chart in them, such as a Macbeth chart. Or is there some other feature in the photos that is known to remain unchanged so that it may be used as a reference?  On the other hand, if they were really taken under standard conditions, why not simply measure the intensities of each coral and see if the errors fall out when averages are done?
>>>
>>> I had a case a few years ago where someone came to me with about a thousand poorly lit and compressed jpeg files that they wanted to quantify.  I had to ask, why didn't you ask about this BEFORE you shot the pictures?  Or three years ago when you wrote the grant application?  I know that we often come up with nifty ideas for analysis after we have the data, but in a case like this the problem must have been defined in advance.
>>>
>>> Ok, enough preaching.  Now maybe someone could practically help Blake...
>>>
>>> ________________________________________________________
>>> Michael Cammer, Assistant Research Scientist Skirball Institute of Biomolecular Medicine
>>> Lab: [phone]  Cell: [phone]
>>>
>>> -----Original Message-----
>>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Blake Elder
>>> Sent: Wednesday, February 08, 2012 10:05 PM
>>> To: [hidden email]
>>> Subject: imageJ use?
>>>
>>> Hi
>>>
>>> I'm an marine science undergraduate with roughly 600 pictures of coral samples that need to be quantified for bleaching. I was wondering if there is a process in ImageJ that I could use to uniquely identify the color of each sample in relation to all of the other pictures. This value would have to be something I can use to determine if bleaching was worse in some samples compared to others. All pictures were taken in a standardized view and lighting but I may also need to correct for slight glares, shading, etc. from picture to picture in the analysis.
>>>
>>> I'm very new to the software and appreciate any help offered.
>>>
>>> Anyone have any ideas?
>>>
>>> Thanks
>>> Blake
>>>
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>>> =================================