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"parula" LUT?

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lechristophe

"parula" LUT?

Hi,

I quite like the new Matlab default LUT, a blue-yellow gradient named
"parula" which was designed to correct the flaws of the "jet" rainbow lut
(see
http://blogs.mathworks.com/steve/2014/10/13/a-new-colormap-for-matlab-part-1-introduction/).
Would someone by any chance have ported it as an ImageJ ROI already? I'm
not sure to know how to do it, but I found the key color points in the
gnuplot port, so I guess it's a matter of interpolating them into 256
values to get an ImageJ LUT?

Thanks for your help,

Christophe

# palette
set palette defined (\
0 0.2081 0.1663 0.5292,\
1 0.2116 0.1898 0.5777,\
2 0.2123 0.2138 0.6270,\
3 0.2081 0.2386 0.6771,\
4 0.1959 0.2645 0.7279,\
5 0.1707 0.2919 0.7792,\
6 0.1253 0.3242 0.8303,\
7 0.0591 0.3598 0.8683,\
8 0.0117 0.3875 0.8820,\
9 0.0060 0.4086 0.8828,\
10 0.0165 0.4266 0.8786,\
11 0.0329 0.4430 0.8720,\
12 0.0498 0.4586 0.8641,\
13 0.0629 0.4737 0.8554,\
14 0.0723 0.4887 0.8467,\
15 0.0779 0.5040 0.8384,\
16 0.0793 0.5200 0.8312,\
17 0.0749 0.5375 0.8263,\
18 0.0641 0.5570 0.8240,\
19 0.0488 0.5772 0.8228,\
20 0.0343 0.5966 0.8199,\
21 0.0265 0.6137 0.8135,\
22 0.0239 0.6287 0.8038,\
23 0.0231 0.6418 0.7913,\
24 0.0228 0.6535 0.7768,\
25 0.0267 0.6642 0.7607,\
26 0.0384 0.6743 0.7436,\
27 0.0590 0.6838 0.7254,\
28 0.0843 0.6928 0.7062,\
29 0.1133 0.7015 0.6859,\
30 0.1453 0.7098 0.6646,\
31 0.1801 0.7177 0.6424,\
32 0.2178 0.7250 0.6193,\
33 0.2586 0.7317 0.5954,\
34 0.3022 0.7376 0.5712,\
35 0.3482 0.7424 0.5473,\
36 0.3953 0.7459 0.5244,\
37 0.4420 0.7481 0.5033,\
38 0.4871 0.7491 0.4840,\
39 0.5300 0.7491 0.4661,\
40 0.5709 0.7485 0.4494,\
41 0.6099 0.7473 0.4337,\
42 0.6473 0.7456 0.4188,\
43 0.6834 0.7435 0.4044,\
44 0.7184 0.7411 0.3905,\
45 0.7525 0.7384 0.3768,\
46 0.7858 0.7356 0.3633,\
47 0.8185 0.7327 0.3498,\
48 0.8507 0.7299 0.3360,\
49 0.8824 0.7274 0.3217,\
50 0.9139 0.7258 0.3063,\
51 0.9450 0.7261 0.2886,\
52 0.9739 0.7314 0.2666,\
53 0.9938 0.7455 0.2403,\
54 0.9990 0.7653 0.2164,\
55 0.9955 0.7861 0.1967,\
56 0.9880 0.8066 0.1794,\
57 0.9789 0.8271 0.1633,\
58 0.9697 0.8481 0.1475,\
59 0.9626 0.8705 0.1309,\
60 0.9589 0.8949 0.1132,\
61 0.9598 0.9218 0.0948,\
62 0.9661 0.9514 0.0755,\
63 0.9763 0.9831 0.0538)

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

Gabriel Landini

Re: "parula" LUT?

On Monday 09 Feb 2015 22:53:25 Christophe Leterrier wrote:

> Hi,
>
> I quite like the new Matlab default LUT, a blue-yellow gradient named
> "parula" which was designed to correct the flaws of the "jet" rainbow lut
> (see
> http://blogs.mathworks.com/steve/2014/10/13/a-new-colormap-for-matlab-part-1
> -introduction/). Would someone by any chance have ported it as an ImageJ ROI
> already? I'm not sure to know how to do it, but I found the key color
> points in the gnuplot port, so I guess it's a matter of interpolating them
> into 256 values to get an ImageJ LUT?

You could scan the image in that link in 256 steps and extract the rgb
components at each location.
See the attached.

Cheers

Gabriel

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

parula.lut (3K) Download Attachment

lechristophe

Re: "parula" LUT?

Thanks a lot Gabriel!

Of note for others interested, the signature :
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

is appended at the end of the lut file when downloaded from Gmail. In case
ImageJ does not recognize the file as a lut, just edit the file to remove
it.

Cheers,

Christophe

On Mon, Feb 9, 2015 at 11:47 PM, Gabriel Landini <[hidden email]>
wrote:

> On Monday 09 Feb 2015 22:53:25 Christophe Leterrier wrote:
> > Hi,
> >
> > I quite like the new Matlab default LUT, a blue-yellow gradient named
> > "parula" which was designed to correct the flaws of the "jet" rainbow lut
> > (see
> >
> http://blogs.mathworks.com/steve/2014/10/13/a-new-colormap-for-matlab-part-1
> > -introduction/). Would someone by any chance have ported it as an ImageJ
> ROI
> > already? I'm not sure to know how to do it, but I found the key color
> > points in the gnuplot port, so I guess it's a matter of interpolating
> them
> > into 256 values to get an ImageJ LUT?
>
> You could scan the image in that link in 256 steps and extract the rgb
> components at each location.
> See the attached.
>
> Cheers
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Cammer, Michael

Re: "parula" LUT?

In reply to this post by lechristophe

In a macro you could parse out the numbers from the text using string functions, multiply each by 255, and then define a LUT.

We did something similar back in the day to grab this LUT from Metamorph.

Or paste into your favorite spreadsheet, do the math, and then type a lot.

//===========================================
macro "Recolor with ratio LUT [F6]"{
requires ('1.38f');
makeFavoriteAIFpseudocolorLUT();
}

//===========================================
function makeFavoriteAIFpseudocolorLUT(){
red = newArray(0,4,8,12,16,20,24,28,32,36,40,44,48,52,56,60,64,68,72,76,80,84,88,92,96,100,104,108,112,116,120,124,128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,120,112,104,96,88,80,72,64,56,48,40,32,24,16,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,7,11,15,19,23,27,31,35,39,43,47,51,55,59,63,67,71,75,79,83,87,91,95,99,103,107,111,115,119,123,127,131,135,139,143,147,151,155,159,163,167,171,175,179,183,187,191,195,199,203,207,211,215,219,223,227,231,235,239,243,247,251,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255);
green = newArray(0,1,2,3,4,5,6,7,8,9,10,9,9,8,8,7,7,6,6,5,5,5,4,4,3,3,2,2,1,1,0,0,0,7,15,23,31,39,47,55,63,71,79,87,95,103,111,119,127,135,143,151,159,167,175,183,191,199,207,215,223,231,239,247,255,247,239,231,223,215,207,199,191,183,175,167,159,151,143,135,128,129,131,132,134,135,137,139,140,142,143,145,147,148,150,151,153,154,156,158,159,161,162,164,166,167,169,170,172,174,175,177,178,180,181,183,185,186,188,189,191,193,194,196,197,199,201,202,204,205,207,208,210,212,213,215,216,218,220,221,223,224,226,228,229,231,232,234,235,237,239,240,242,243,245,247,248,250,251,253,255,251,247,243,239,235,231,227,223,219,215,211,207,203,199,195,191,187,183,179,175,171,167,163,159,155,151,147,143,139,135,131,127,123,119,115,111,107,103,99,95,91,87,83,79,75,71,67,63,59,55,51,47,43,39,35,31,27,23,19,15,11,7,3,0,8,16,24,32,41,49,57,65,74,82,90,98,106,115,123,131,139,148,156,164,172,180,189,197,205,213,222,230,238,246,254);
blue = newArray(0,7,15,23,31,39,47,55,63,71,79,87,95,103,111,119,127,135,143,151,159,167,175,183,191,199,207,215,223,231,239,247,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,251,247,243,239,235,231,227,223,219,215,211,207,203,199,195,191,187,183,179,175,171,167,163,159,155,151,147,143,139,135,131,128,126,124,122,120,118,116,114,112,110,108,106,104,102,100,98,96,94,92,90,88,86,84,82,80,78,76,74,72,70,68,66,64,62,60,58,56,54,52,50,48,46,44,42,40,38,36,34,32,30,28,26,24,22,20,18,16,14,12,10,8,6,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,16,24,32,41,49,57,65,74,82,90,98,106,115,123,131,139,148,156,164,172,180,189,197,205,213,222,230,238,246,254);
setLut(red, green, blue);
}

=========================================================================
Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center
Cell: 914-309-3270 Temporary location: SK2-7
http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Christophe Leterrier
Sent: Monday, February 09, 2015 4:53 PM
To: [hidden email]
Subject: "parula" LUT?

Hi,

I quite like the new Matlab default LUT, a blue-yellow gradient named "parula" which was designed to correct the flaws of the "jet" rainbow lut (see http://blogs.mathworks.com/steve/2014/10/13/a-new-colormap-for-matlab-part-1-introduction/).
Would someone by any chance have ported it as an ImageJ ROI already? I'm not sure to know how to do it, but I found the key color points in the gnuplot port, so I guess it's a matter of interpolating them into 256 values to get an ImageJ LUT?

Thanks for your help,

Christophe

# palette
set palette defined (\
0 0.2081 0.1663 0.5292,\
1 0.2116 0.1898 0.5777,\
2 0.2123 0.2138 0.6270,\
3 0.2081 0.2386 0.6771,\
4 0.1959 0.2645 0.7279,\
5 0.1707 0.2919 0.7792,\
6 0.1253 0.3242 0.8303,\
7 0.0591 0.3598 0.8683,\
8 0.0117 0.3875 0.8820,\
9 0.0060 0.4086 0.8828,\
10 0.0165 0.4266 0.8786,\
11 0.0329 0.4430 0.8720,\
12 0.0498 0.4586 0.8641,\
13 0.0629 0.4737 0.8554,\
14 0.0723 0.4887 0.8467,\
15 0.0779 0.5040 0.8384,\
16 0.0793 0.5200 0.8312,\
17 0.0749 0.5375 0.8263,\
18 0.0641 0.5570 0.8240,\
19 0.0488 0.5772 0.8228,\
20 0.0343 0.5966 0.8199,\
21 0.0265 0.6137 0.8135,\
22 0.0239 0.6287 0.8038,\
23 0.0231 0.6418 0.7913,\
24 0.0228 0.6535 0.7768,\
25 0.0267 0.6642 0.7607,\
26 0.0384 0.6743 0.7436,\
27 0.0590 0.6838 0.7254,\
28 0.0843 0.6928 0.7062,\
29 0.1133 0.7015 0.6859,\
30 0.1453 0.7098 0.6646,\
31 0.1801 0.7177 0.6424,\
32 0.2178 0.7250 0.6193,\
33 0.2586 0.7317 0.5954,\
34 0.3022 0.7376 0.5712,\
35 0.3482 0.7424 0.5473,\
36 0.3953 0.7459 0.5244,\
37 0.4420 0.7481 0.5033,\
38 0.4871 0.7491 0.4840,\
39 0.5300 0.7491 0.4661,\
40 0.5709 0.7485 0.4494,\
41 0.6099 0.7473 0.4337,\
42 0.6473 0.7456 0.4188,\
43 0.6834 0.7435 0.4044,\
44 0.7184 0.7411 0.3905,\
45 0.7525 0.7384 0.3768,\
46 0.7858 0.7356 0.3633,\
47 0.8185 0.7327 0.3498,\
48 0.8507 0.7299 0.3360,\
49 0.8824 0.7274 0.3217,\
50 0.9139 0.7258 0.3063,\
51 0.9450 0.7261 0.2886,\
52 0.9739 0.7314 0.2666,\
53 0.9938 0.7455 0.2403,\
54 0.9990 0.7653 0.2164,\
55 0.9955 0.7861 0.1967,\
56 0.9880 0.8066 0.1794,\
57 0.9789 0.8271 0.1633,\
58 0.9697 0.8481 0.1475,\
59 0.9626 0.8705 0.1309,\
60 0.9589 0.8949 0.1132,\
61 0.9598 0.9218 0.0948,\
62 0.9661 0.9514 0.0755,\
63 0.9763 0.9831 0.0538)

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

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

Lachlan Whitehead

Re: "parula" LUT?

Before going ahead with this, it's probably worth considering the IP implications.

Steve Eddins has responded to similar requests in the past with:

"... /Parula is the end result of a creative design effort over
an extended period of time. I am pleased that you find it so
appealing. The colormap is, however, MathWorks intellectual
property, and it would not be appropriate or acceptable to copy or
re-use it in non-MathWorks plotting tools."

While I'm (almost) sure there would be no legal followup, I think it's worth keeping in mind.

----- Original Message -----
From: "Michael Cammer" <[hidden email]>
To: [hidden email]
Sent: Tuesday, 10 February, 2015 10:03:55 AM
Subject: Re: "parula" LUT?

In a macro you could parse out the numbers from the text using string functions, multiply each by 255, and then define a LUT.

We did something similar back in the day to grab this LUT from Metamorph.

Or paste into your favorite spreadsheet, do the math, and then type a lot.

//===========================================
macro "Recolor with ratio LUT [F6]"{
requires ('1.38f');
makeFavoriteAIFpseudocolorLUT();
}

//===========================================
function makeFavoriteAIFpseudocolorLUT(){
red = newArray(0,4,8,12,16,20,24,28,32,36,40,44,48,52,56,60,64,68,72,76,80,84,88,92,96,100,104,108,112,116,120,124,128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,120,112,104,96,88,80,72,64,56,48,40,32,24,16,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,7,11,15,19,23,27,31,35,39,43,47,51,55,59,63,67,71,75,79,83,87,91,95,99,103,107,111,115,119,123,127,131,135,139,143,147,151,155,159,163,167,171,175,179,183,187,191,195,199,203,207,211,215,219,223,227,231,235,239,243,247,251,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255);
green = newArray(0,1,2,3,4,5,6,7,8,9,10,9,9,8,8,7,7,6,6,5,5,5,4,4,3,3,2,2,1,1,0,0,0,7,15,23,31,39,47,55,63,71,79,87,95,103,111,119,127,135,143,151,159,167,175,183,191,199,207,215,223,231,239,247,255,247,239,231,223,215,207,199,191,183,175,167,159,151,143,135,128,129,131,132,134,135,137,139,140,142,143,145,147,148,150,151,153,154,156,158,159,161,162,164,166,167,169,170,172,174,175,177,178,180,181,183,185,186,188,189,191,193,194,196,197,199,201,202,204,205,207,208,210,212,213,215,216,218,220,221,223,224,226,228,229,231,232,234,235,237,239,240,242,243,245,247,248,250,251,253,255,251,247,243,239,235,231,227,223,219,215,211,207,203,199,195,191,187,183,179,175,171,167,163,159,155,151,147,143,139,135,131,127,123,119,115,111,107,103,99,95,91,87,83,79,75,71,67,63,59,55,51,47,43,39,35,31,27,23,19,15,11,7,3,0,8,16,24,32,41,49,57,65,74,82,90,98,106,115,123,131,139,148,156,164,172,180,189,197,205,213,222,230,238,246,254);
blue = newArray(0,7,15,23,31,39,47,55,63,71,79,87,95,103,111,119,127,135,143,151,159,167,175,183,191,199,207,215,223,231,239,247,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,251,247,243,239,235,231,227,223,219,215,211,207,203,199,195,191,187,183,179,175,171,167,163,159,155,151,147,143,139,135,131,128,126,124,122,120,118,116,114,112,110,108,106,104,102,100,98,96,94,92,90,88,86,84,82,80,78,76,74,72,70,68,66,64,62,60,58,56,54,52,50,48,46,44,42,40,38,36,34,32,30,28,26,24,22,20,18,16,14,12,10,8,6,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,16,24,32,41,49,57,65,74,82,90,98,106,115,123,131,139,148,156,164,172,180,189,197,205,213,222,230,238,246,254);
setLut(red, green, blue);
}

=========================================================================
Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center
Cell: 914-309-3270 Temporary location: SK2-7
http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Christophe Leterrier
Sent: Monday, February 09, 2015 4:53 PM
To: [hidden email]
Subject: "parula" LUT?

Hi,

I quite like the new Matlab default LUT, a blue-yellow gradient named "parula" which was designed to correct the flaws of the "jet" rainbow lut (see http://blogs.mathworks.com/steve/2014/10/13/a-new-colormap-for-matlab-part-1-introduction/).
Would someone by any chance have ported it as an ImageJ ROI already? I'm not sure to know how to do it, but I found the key color points in the gnuplot port, so I guess it's a matter of interpolating them into 256 values to get an ImageJ LUT?

Thanks for your help,

Christophe

# palette
set palette defined (\
0 0.2081 0.1663 0.5292,\
1 0.2116 0.1898 0.5777,\
2 0.2123 0.2138 0.6270,\
3 0.2081 0.2386 0.6771,\
4 0.1959 0.2645 0.7279,\
5 0.1707 0.2919 0.7792,\
6 0.1253 0.3242 0.8303,\
7 0.0591 0.3598 0.8683,\
8 0.0117 0.3875 0.8820,\
9 0.0060 0.4086 0.8828,\
10 0.0165 0.4266 0.8786,\
11 0.0329 0.4430 0.8720,\
12 0.0498 0.4586 0.8641,\
13 0.0629 0.4737 0.8554,\
14 0.0723 0.4887 0.8467,\
15 0.0779 0.5040 0.8384,\
16 0.0793 0.5200 0.8312,\
17 0.0749 0.5375 0.8263,\
18 0.0641 0.5570 0.8240,\
19 0.0488 0.5772 0.8228,\
20 0.0343 0.5966 0.8199,\
21 0.0265 0.6137 0.8135,\
22 0.0239 0.6287 0.8038,\
23 0.0231 0.6418 0.7913,\
24 0.0228 0.6535 0.7768,\
25 0.0267 0.6642 0.7607,\
26 0.0384 0.6743 0.7436,\
27 0.0590 0.6838 0.7254,\
28 0.0843 0.6928 0.7062,\
29 0.1133 0.7015 0.6859,\
30 0.1453 0.7098 0.6646,\
31 0.1801 0.7177 0.6424,\
32 0.2178 0.7250 0.6193,\
33 0.2586 0.7317 0.5954,\
34 0.3022 0.7376 0.5712,\
35 0.3482 0.7424 0.5473,\
36 0.3953 0.7459 0.5244,\
37 0.4420 0.7481 0.5033,\
38 0.4871 0.7491 0.4840,\
39 0.5300 0.7491 0.4661,\
40 0.5709 0.7485 0.4494,\
41 0.6099 0.7473 0.4337,\
42 0.6473 0.7456 0.4188,\
43 0.6834 0.7435 0.4044,\
44 0.7184 0.7411 0.3905,\
45 0.7525 0.7384 0.3768,\
46 0.7858 0.7356 0.3633,\
47 0.8185 0.7327 0.3498,\
48 0.8507 0.7299 0.3360,\
49 0.8824 0.7274 0.3217,\
50 0.9139 0.7258 0.3063,\
51 0.9450 0.7261 0.2886,\
52 0.9739 0.7314 0.2666,\
53 0.9938 0.7455 0.2403,\
54 0.9990 0.7653 0.2164,\
55 0.9955 0.7861 0.1967,\
56 0.9880 0.8066 0.1794,\
57 0.9789 0.8271 0.1633,\
58 0.9697 0.8481 0.1475,\
59 0.9626 0.8705 0.1309,\
60 0.9589 0.8949 0.1132,\
61 0.9598 0.9218 0.0948,\
62 0.9661 0.9514 0.0755,\
63 0.9763 0.9831 0.0538)

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dksamuel

Re: "parula" LUT?

In reply to this post by lechristophe

Christophe, while IP issues are there thanks for the advice, wanted this
lut for a long time, Dr.D.K.Samuel, Bangalore, India
[image: Inline image 1]

On Tue, Feb 10, 2015 at 4:28 AM, Christophe Leterrier <
[hidden email]> wrote:

> Thanks a lot Gabriel!
>
> Of note for others interested, the signature :
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> is appended at the end of the lut file when downloaded from Gmail. In case
> ImageJ does not recognize the file as a lut, just edit the file to remove
> it.
>
> Cheers,
>
> Christophe
>
> On Mon, Feb 9, 2015 at 11:47 PM, Gabriel Landini <[hidden email]>
> wrote:
>
> > On Monday 09 Feb 2015 22:53:25 Christophe Leterrier wrote:
> > > Hi,
> > >
> > > I quite like the new Matlab default LUT, a blue-yellow gradient named
> > > "parula" which was designed to correct the flaws of the "jet" rainbow
> lut
> > > (see
> > >
> >
> http://blogs.mathworks.com/steve/2014/10/13/a-new-colormap-for-matlab-part-1
> > > -introduction/). Would someone by any chance have ported it as an
> ImageJ
> > ROI
> > > already? I'm not sure to know how to do it, but I found the key color
> > > points in the gnuplot port, so I guess it's a matter of interpolating
> > them
> > > into 256 values to get an ImageJ LUT?
> >
> > You could scan the image in that link in 256 steps and extract the rgb
> > components at each location.
> > See the attached.
> >
> > Cheers
> >
> > Gabriel
> >
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> >
>
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