Need Help : About Values Selection
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Need Help : About Values Selection
 
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Dear all,
I have 2048 X 2048 resolution grayscale images, each coordinates have it's own gray values. I have two problem here, first is how to select all pixel with specific gray values and second is how to change it's colors. The purpose this work is to give marks to parts of image with different values. For Example : The part of Image that have Gray Value 0-100 will have blue color, and another values will set to red colour. Can i do that ? I'm new at ImageJ. Can anyone help me to do this ? Thanks for your attention. Best Regards, Ekoputra A.B. Student of Mining Engineering Institute Technology of Bandung (ITB) Indonesia |
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Hi, You can either threshold your image by going into the image menu and choosing Adjust and then Threshold, you can then change the range of threshold you need. The other alternative to coloring is for you to use the image menu again, go into Lookup Tables and then choose which color you want to use. I do hope this olves your problem. |
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In reply to this post by Ekoputra A.B.
Hi, You can either threshold your image by going into the image menu and choosing Adjust and then Threshold, you can then change the range of threshold you need. The other alternative to coloring is for you to use the image menu again, go into Lookup Tables and then choose which color you want to use. I do hope this olves your problem. |
Re: Need Help : About Values Selection
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In reply to this post by Ekoputra A.B.
I hope I'm not committing a faux pas by suggesting that it might be easier
for you to do this in Photoshop: First make your image of the type "Indexed color" (Image > Mode > Indexed Color). Now, under Image > Mode > Color Table you can display a table of the colors (or shades of gray) assigned to each intensity value 0-255; bottom right square is 0, top left is 255. Click on an square to choose a new color for that corresponding intensity value. You'll have to go through each and every square manually to change the colors, but once you've done it once you can save the new color table to apply it to other images. -Esteban On Tue, Dec 30, 2008 at 4:54 AM, Ekoputra A.B. <[hidden email]>wrote: > Dear all, > > I have 2048 X 2048 resolution grayscale images, each coordinates have it's > own gray values. > I have two problem here, first is how to select all pixel with specific > gray > values and second is how to change it's colors. > The purpose this work is to give marks to parts of image with different > values. > For Example : The part of Image that have Gray Value 0-100 will have blue > color, and another values will set to red colour. Can i do that ? > > I'm new at ImageJ. Can anyone help me to do this ? Thanks for your > attention. > > Best Regards, > > > Ekoputra A.B. > Student of Mining Engineering > Institute Technology of Bandung (ITB) > Indonesia > -- > View this message in context: > http://n2.nabble.com/Need-Help-%3A-About-Values-Selection-tp2091973p2091973.html > Sent from the ImageJ mailing list archive at Nabble.com. > -- G. Esteban Fernandez, Ph.D. Associate Director Molecular Cytology Core Facility University of Missouri 120 Bond Life Sciences Center Columbia, MO 65211 http://www.biotech.missouri.edu/mcc/ 573-882-4895 573-884-9395 fax |
Re: Need Help : About Values Selection
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In reply to this post by Ekoputra A.B.
On Dec 30, 2008, at 5:54 AM, Ekoputra A.B. wrote:
> Dear all, > > I have 2048 X 2048 resolution grayscale images, each coordinates have > it's > own gray values. > I have two problem here, first is how to select all pixel with > specific gray > values and second is how to change it's colors. > The purpose this work is to give marks to parts of image with different > values. > For Example : The part of Image that have Gray Value 0-100 will have > blue > color, and another values will set to red colour. Can i do that ? > > I'm new at ImageJ. Can anyone help me to do this ? Thanks for your > attention. You can do this using ImageJ's LUT Editor: 1. Open the LUT Editor using Image>Color>Edit LUT 2. Drag from the first LUT index (the one in the upper left corner) to the 100th 3. Select red=0, green=0, blue=255 in the first color picker 4. Select red=0, green=0, blue=255 in the second 5. Drag from index 101 to the last index (the one in the lower right corner) 6. Select red=255, green=0, blue=0 in the first color picker 7. Select red=255, green=0, blue=0 in the second Note that the LUT indexes are displayed in the ImageJ status bar as you move the mouse over the LUT Editor grid. Index 100 is in the 5th column and 7th row of the grid. In ImageJ 1.42f and later, the indexes are displayed in the status bar while you drag across the grid. -wayne |
Re: Need Help : About Values Selection
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Dear All,
Thanks to all who has responsed for my questions, I've tried the Look up table. But i have a problem here, The Gray value on my images has high range of the value, about -400 till 1500. But if i use the Look up Table, the range of value is just 0-255. Is there any correlation with value on Look up Table and gray value on my images ? I want to change color of specific gray value on my images. Best Regards, Ekoputra A.B. |
Re: Need Help : About Values Selection
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What is the bit depth and format of your images? Could you post one?
> Dear All, > > Thanks to all who has responsed for my questions, I've tried the Look up > table. But i have a problem here, The Gray value on my images has high range > of the value, about -400 till 1500. But if i use the Look up Table, the > range of value is just 0-255. > Is there any correlation with value on Look up Table and gray value on my > images ? > I want to change color of specific gray value on my images. > > Best Regards, > > > Ekoputra A.B. > -- > View this message in context: http://n2.nabble.com/Need-Help-%3A-About-Values-Selection-tp2091973p2095073.html > Sent from the ImageJ mailing list archive at Nabble.com. -- Joel B. Sheffield, Ph.D. Biology Department, Temple University 1900 North 12th Street Philadelphia, PA 19122 [hidden email] (215) 204 8839, fax (215) 204 0486 http://astro.temple.edu/~jbs |
Re: Need Help : About Values Selection
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Dear Joel,
Thanks for your explanation about LUT. I have tried this to my Images, and i think it is can be done with 32 bit images. by using a *.txt file as a LUT, can change the color without change image's gray values. but i can't find a way to solving my problem, the problem is to correlate the gray value to LUT. Mr. Wayne tells about using : v2 = (v1+400)*(255/1900) to convert a value (v1) in an image with a range of -400 to 1500 to a value (v2) in the range 0 to 255. But i still confused what i should do with this. Any advices or suggestion on this one? it is very help me. Thanks 2009/1/3 Joel Sheffield <jbs@temple.edu> In principle, yes. I haven't done it with 32 bit images, but with 8- bit, you make a table in excell, first column numbers from 1-256, (index), second, for the red channel, either 0 or 255 depending on whether you want those pixels to be red (255means red), third channel, similarly for green, but with zeroes where the other column is red, and the fourth channel for blue, Save this as a .txt file, and then import it into ImageJ as a lut. As I said, I don't have experience with the 32-bit format, so I can't give you advice on that one. You might try converting the 32 to 8 bit, and then try the scan, and the lut. -------------- Original message --------------- Date sent: Sat, 3 Jan 2009 17:24:31 +0700 From: "Ekoputra Arif Budiman" <ekoputra.ab@gmail.com> To: jbs@temple.edu Subject: Re: Need Help : About Values Selection From: "Ekoputra Arif Budiman" <ekoputra.ab@gmail.com><br> To: jbs@temple.edu<br> Subject: Re: Need Help : About Values Selection<br> To: <a<br> Hi, Thanks for your explanations about LUT table. I think with LUT table, it can solve my problem. I've tried this, but once again there is a problem to select pixels with the specific values. Here is my problem : For example, if i take some part of the image using line and do some profiling then i will have this value : 0 537.000000000 1 223.213668823 2 194.641021729 3 174.153839111 4 54.948719025 5 -3.025640965 6 101.076919556 7 48.871795654 8 21.427350998 9 -53.307693481 10 -13.324786186 11 -89.034187317 12 -230.846160889 13 -256.777770996 14 -366.094024658 15 -256.461547852 16 -322.136749268 17 -155.863250732 18 -24.538461685 19 -77.794868469 20 -3.051282167 21 61.615383148 22 97.905982971 23 207.418807983 24 414.153839111 25 432.982910156 26 407.111114502 27 260.923065186 28 168.341873169 29 40.641025543 30 -33.384616852 31 64.888885498 32 128.273498535 33 180.538467407 34 221.239318848 35 256.059814453 36 149.692306519 37 30.555555344 38 -26.709402084 39 -87.000000000 40 -311.589752197 41 -253.384613037 42 -100.923080444 43 170.666671753 44 160.170944214 45 289.307678223 46 405.051269531 47 437.512817383 48 395.923065186 49 319.290588379 50 274.358978271 51 300.230773926 52 197.333328247 53 186.632476807 54 241.000000000 55 198.948715210 56 312.683746338 57 327.384613037 58 360.641021729 59 265.213684082 60 92.230766296 61 -21.923076630 62 -118.529914856 63 -119.000000000 64 -14.846154213 65 53.444442749 66 -11.384614944 67 203.119659424 68 197.735046387 69 218.076919556 70 318.923065186 71 450.341888428 72 465.000000000 73 402.418792725 74 330.529907227 75 461.384613037 76 338.085479736 77 244.162399292 78 145.000000000 79 8.008546829 80 -120.162391663 81 -161.000000000 82 -51.854701996 83 -134.008544922 84 -68.923080444 85 -18.743589401 86 152.461532593 87 306.923065186 88 432.188049316 89 549.170959473 90 801.384643555 91 863.888916016 92 999.239318848 93 1049.384643555 94 1072.470092773 95 1027.333374023 96 1025.076904297 97 846.111083984 98 770.965820312 99 703.615356445 100 650.162414551 As we can see, there are 2 column, First column is coordinates, and the second one is describe to gray value. Based on gray value above, i want to classifying gray value by the colors. The parameters is given as follows: for gray values less than zero = Red for gray values running from 0 to 600 = Green for gray values 600 above = Blue Can i using the Look up Table to do that for the whole images? so the result will consist only for 3 color : red( R=249, G=0, B=0), Green (R=0, G=249, B=0) and Blue (R=0, G=0, B=249) or is it need the macros to do this ? Any advice and suggestions are welcome. Best Regards, Ekoputra A.B. 2009/1/2 Joel Sheffield <jbs@temple.edu> Oh, I'm sorry. I forgot to answer your questions. Check below: -------------- Original message --------------- Date sent: Fri, 2 Jan 2009 17:01:44 +0700 From: "Ekoputra Arif Budiman" <ekoputra.ab@gmail.com> To: jbs@temple.edu Subject: Re: Need Help : About Values Selection From: "Ekoputra Arif Budiman" < ekoputra.ab@gmail.com><br> To: jbs@temple.edu<br> Subject: Re: Need Help : About Values Selection<br> hi, Thanks for your kindly explanations. This is exactly what i need because I want to classify the region of image by it's value and also i want to describe the value by difference color. My expectation is to resulting the image just like yours. The object of my research is in the middle region (the red colour, based on your image). I think i need some way to separate this region. Any advise for this problem is welcome. FYI, my ImageJ version is 1.41o Now, based on your Image, I have a few questions : 1. At your image, I found some values difference ( running from 2 to 255 ). Can i change the color without changing it's value ? Because in my research, the gray value represents CT value of sample. So I need to keep the value as same as it is. ***When you use a lookup table, all you do is change the color associated with a different value. You do not change the values themselves. However, if you change the brightness/contrast, you will cause a change in the original image. 2. Based on your image, is it the changing of colors based on gray value? or else? Yes. The color is assigned because of the gray scale. 3. Can you explain how to do your works on the image, step by step ? it's very helpful, because i am new at this. Thanks for your help. Happy new year 2009. Best Regards, Ekoputra A.B. 2009/1/1 Joel Sheffield <jbs@temple.edu> Hi, When I open the tiff image in my version of ImageJ (1.42f), it opens with a 32-bit presentation with values running from -1758 to 1345, with the in which the negative values are for the black regions of the image, and the background appears to be 0.0. If I run Analyze>histogram, you can see the range of distribution. You can get even a better sense by choosing the "Log" option on the histogram window. I am still unsure what you are trying to measure. I see a circular object on a smooth background. The circular object has pixels of different values, in a large range. Within the circular object there are two dark lines that separate a middle region from the two sides. The mean pixel value in the central region appears to be lower than the sides, but this is based more on the number of pixels than their values. At any rate, I selected one of the luts from the list, and got the enclosed image (in jpg, rgb format just for convenience). It seems to isolate one region from the other. Also, there seems to be no advantage in keeping the image in 32 bit format. You can easily convert it to 8-bit. Make a copy of the image, and select Image>type Is this helpful? -------------- Original message --------------- Date sent: Thu, 1 Jan 2009 15:50:55 +0700 From: "Ekoputra Arif Budiman" <ekoputra.ab@gmail.com> To: jbs@temple.edu Subject: Re: Need Help : About Values Selection Dear All, i've realized that convert the format to JPEG will change the current gray value. So this is the Image with TIF format. I've check the value, and there is no change in it's gray value. I hope you can ignore previous image. Thanks for your attention. Best Regards, Ekoputra A.B. 2009/1/1 Ekoputra Arif Budiman <ekoputra.ab@gmail.com> Dear Joel, It is 32 bit RAW image that i converted to JPEG format. This is the image. Best Regard, Ekoputra A.B. 2009/1/1 Joel Sheffield <jbs@temple.edu> What is the bit depth and format of your images? Could you post one? > Dear All, > > Thanks to all who has responsed for my questions, I've tried the Look up > table. But i have a problem here, The Gray value on my images has high range > of the value, about -400 till 1500. But if i use the Look up Table, the > range of value is just 0-255. > Is there any correlation with value on Look up Table and gray value on my > images ? > I want to change color of specific gray value on my images. > > Best Regards, > > > Ekoputra A.B. > -- > View this message in context: http://n2.nabble.com/Need-Help- %3A- About-Values-Selection-tp2091973p2095073.html > Sent from the ImageJ mailing list archive at Nabble.com. -- Joel B. Sheffield, Ph.D. Biology Department, Temple University 1900 North 12th Street Philadelphia, PA 19122 jbs@temple.edu (215) 204 8839, fax (215) 204 0486 http://astro.temple.edu/~jbs |
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