Heat Maps in ImageJ

[Jacob Keller]

Hi All,

is there a simple way to input a 2D array of values into imageJ, then
display the result as an image colored appropriately? I realize that this
is really what all images are, but I am not sure how to input the array as
numbers into imageJ.

Jacob

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*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [hidden email]
*******************************************

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[ctrueden]

Hi Jacob,

> is there a simple way to input a 2D array of values into imageJ

If you write the numbers in a text file (tab separated, with a newline
between lines), then you can import it using File > Import > Text Image. If
you want to see a working example of the format, you can generate one by
running File > Open Samples > Blobs and then File > Save As > Text Image.

> then display the result as an image colored appropriately?

You can then colorize the image however you want by choosing from the Image
> Lookup Tables menu. Maybe you want "Fire" for a heat map?

-Curtis


On Thu, Jun 21, 2012 at 12:30 PM, Jacob Keller <
[hidden email]> wrote:

> Hi All,
>
> is there a simple way to input a 2D array of values into imageJ, then
> display the result as an image colored appropriately? I realize that this
> is really what all images are, but I am not sure how to input the array as
> numbers into imageJ.
>
> Jacob
>
> --
> *******************************************
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: [hidden email]
> *******************************************
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Stephan Saalfeld]

Hi Jacob,

write the numbers into a text file like

123 45 67 76
234 654 345 456
234 3 34 45

and open that by Import > Text Image...

Then apply the hottest Lookup Table you can find.

Best,
Stephan




On Thu, 2012-06-21 at 12:30 -0500, Jacob Keller wrote:
> Hi All,
>
> is there a simple way to input a 2D array of values into imageJ, then
> display the result as an image colored appropriately? I realize that this
> is really what all images are, but I am not sure how to input the array as
> numbers into imageJ.
>
> Jacob
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Jacob Keller]

Great--works like a dream! Now, to pick my LUT....!

Jacob

On Thu, Jun 21, 2012 at 12:34 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Jacob,
>
> > is there a simple way to input a 2D array of values into imageJ
>
> If you write the numbers in a text file (tab separated, with a newline
> between lines), then you can import it using File > Import > Text Image. If
> you want to see a working example of the format, you can generate one by
> running File > Open Samples > Blobs and then File > Save As > Text Image.
>
> > then display the result as an image colored appropriately?
>
> You can then colorize the image however you want by choosing from the Image
> > Lookup Tables menu. Maybe you want "Fire" for a heat map?
>
> -Curtis
>
>
> On Thu, Jun 21, 2012 at 12:30 PM, Jacob Keller <
> [hidden email]> wrote:
>
> > Hi All,
> >
> > is there a simple way to input a 2D array of values into imageJ, then
> > display the result as an image colored appropriately? I realize that this
> > is really what all images are, but I am not sure how to input the array
> as
> > numbers into imageJ.
> >
> > Jacob
> >
> > --
> > *******************************************
> > Jacob Pearson Keller
> > Northwestern University
> > Medical Scientist Training Program
> > email: [hidden email]
> > *******************************************
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [hidden email]
*******************************************

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Robert Dougherty]

Jacob,

I think Red Hot is the best.  It looks like a thermal scale. I remember a paper by Victor Sparrow at Penn State University in about 1996 in which he studied the issue and decided that a thermal scale is the best because it still works when printed or copied in B&W and because it makes sense to color blind viewers.  Naturally I can't find the paper now.

Bob



On Jun 21, 2012, at 11:47 AM, Jacob Keller wrote:

> Great--works like a dream! Now, to pick my LUT....!
>
> Jacob
>
> On Thu, Jun 21, 2012 at 12:34 PM, Curtis Rueden <[hidden email]> wrote:
>
>> Hi Jacob,
>>
>>> is there a simple way to input a 2D array of values into imageJ
>>
>> If you write the numbers in a text file (tab separated, with a newline
>> between lines), then you can import it using File > Import > Text Image. If
>> you want to see a working example of the format, you can generate one by
>> running File > Open Samples > Blobs and then File > Save As > Text Image.
>>
>>> then display the result as an image colored appropriately?
>>
>> You can then colorize the image however you want by choosing from the Image
>>> Lookup Tables menu. Maybe you want "Fire" for a heat map?
>>
>> -Curtis
>>
>>
>> On Thu, Jun 21, 2012 at 12:30 PM, Jacob Keller <
>> [hidden email]> wrote:
>>
>>> Hi All,
>>>
>>> is there a simple way to input a 2D array of values into imageJ, then
>>> display the result as an image colored appropriately? I realize that this
>>> is really what all images are, but I am not sure how to input the array
>> as
>>> numbers into imageJ.
>>>
>>> Jacob
>>>
>>> --
>>> *******************************************
>>> Jacob Pearson Keller
>>> Northwestern University
>>> Medical Scientist Training Program
>>> email: [hidden email]
>>> *******************************************
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>
> --
> *******************************************
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: [hidden email]
> *******************************************
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Robert Dougherty, Ph.D.
President, OptiNav, Inc.
1414 127th Place NE #106
Bellevue, WA 98005
Tel. [phone]
FAX [phone]
www.optinav.com
[hidden email]

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[Gabriel Landini]

On Thursday 21 Jun 2012 20:09:04 Robert Dougherty wrote:
> I think Red Hot is the best.  It looks like a thermal scale. I remember a
> paper by Victor Sparrow at Penn State University in about 1996 in which he
> studied the issue and decided that a thermal scale is the best because it
> still works when printed or copied in B&W and because it makes sense to
> color blind viewers.  Naturally I can't find the paper now.

Maybe it it the paper below? Unfortunately our library does not carry that
journal, but it looks interesting.
Regards

Gabriel

The use of color in the scientific visualization of acoustical phenomena
Sparrow, VW; Rochat, JL; Bard, BA
JOURNAL OF COMPUTATIONAL ACOUSTICS  Volume: 4   Issue: 2   Pages: 203-223  
DOI: 10.1142/S0218396X96000052   Published: JUN 1996

Abstract: Color is commonly used in representing scientific data, especially
as color output devices have become widely available. The misuse of color can
lead to confusing or even misleading representations of data. The purpose of
this paper is to provide a review of guidelines for using color effectively,
specifically aimed at the computational acoustics community. The question of
whether or not to use color at all is initially raised, and gray-scale is
suggested for appropriate cases. Human color deficiencies in technical
audiences are then described, and the consequential choices of equally-
accessible color schemes are discussed. The topics of human color perception
models, hypsometric tints, contoured plots, and histogram equalization are
introduced. Color palettes specifically suited for acoustical phenomena, such
as linear and dB magnitudes, scales for positive and negative data, circular
palettes for phase, and methods for illustrating different classes of
phenomena (e.g., wave types) on a single plot, are discussed in detail. Color
examples and Mathematica code are provided, and final recommendations are made
for choosing effective color schemes.

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