Re: Totally new here. Color Counter question
Posted by Robert Smith on Oct 16, 2019; 1:52am
URL: http://imagej.273.s1.nabble.com/Totally-new-here-Color-Counter-question-tp5022515p5022545.html
Hello Emily Teng,
Attached you will find a 'macro' which is a small subprogram to Fiji/ImageJ which will do as I described.
You will need to download and copy it.
Goto Plugins > New > Macro and click it. It will open a notepad type page. Paste your copy onto the page, save it as "Image Expression" in the Fiji/ImageJ folder - Macros in the Fiji/ImageJ app on your computer.
Then goto Plugins > Macros > Install, choose it from the list and click it. This will install it in your Plugins > Macros tab. Now each time you need to use it use Plugins > Image Expression and run it by clicking it. You will probably see how it is used just by looking at it, but if not then just type back at me and describe the situation and we will work on it, but I doubt you will have any problems.
You will have to install it every time you start ImageJ but only once. Then you can decide if you want to install it permantly.
You are correct that the expression is entered once you run it. You will see where to assign the color channels there also.
I personally use a custom LUT, but it is simply the listed "Physics" LUT inverted. If you use the standard Physics LUT, then the Red colors are the highest intensity and the Blue colors as the darkest or black pixels. Use Analyze > Histogram to see which and how many pixels are depicted. You should also probably use a copy of your processed image prior to adding the LUT to compare to until you get used to reading the Histogram, but that shouldn't take long.
It may sound complicated at first but it isn't so don't get excited or discouraged as you go, I know you can do it.
Any other questions or problems then just let me know.
Bob
________________________________
From: Emily Teng <[hidden email]>
Sent: Tuesday, October 15, 2019 6:26 PM
To: [hidden email] <[hidden email]>
Subject: Re: Totally new here. Color Counter question
Dear Bob,
Thank you so much for your suggestions. Unfortunately, I am very ignorant on how to use the program. I don't know how to do most of you what you suggested. First:
Process > Image Expression Parser(Macro). Where is this? Something I need to add? I do know how to split the channels. ( Image > Color > Split Channels (make sure to keep the original)) but not how to use the parser macro to assign Red to A, Green to B, and Blue to C.
I guess the parser macro is where I am supposed to "Enter the equation in the field ,,,Sqrt(1-(A*A)/(B*B))?"
I see there are many LUTs but I don't know how to use them.
If you have the time and could give more detailed step by steps on how to do this, I would really appreciate it. I am learning, but have literally just downloaded the program a week ago and looked at a few tutorials so really know next to nothing....
Thank you so much.
Emily
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ImageJ mailing list: http://imagej.nih.gov/ij/list.html
URL: http://imagej.273.s1.nabble.com/Totally-new-here-Color-Counter-question-tp5022515p5022545.html
Hello Emily Teng,
Attached you will find a 'macro' which is a small subprogram to Fiji/ImageJ which will do as I described.
You will need to download and copy it.
Goto Plugins > New > Macro and click it. It will open a notepad type page. Paste your copy onto the page, save it as "Image Expression" in the Fiji/ImageJ folder - Macros in the Fiji/ImageJ app on your computer.
Then goto Plugins > Macros > Install, choose it from the list and click it. This will install it in your Plugins > Macros tab. Now each time you need to use it use Plugins > Image Expression and run it by clicking it. You will probably see how it is used just by looking at it, but if not then just type back at me and describe the situation and we will work on it, but I doubt you will have any problems.
You will have to install it every time you start ImageJ but only once. Then you can decide if you want to install it permantly.
You are correct that the expression is entered once you run it. You will see where to assign the color channels there also.
I personally use a custom LUT, but it is simply the listed "Physics" LUT inverted. If you use the standard Physics LUT, then the Red colors are the highest intensity and the Blue colors as the darkest or black pixels. Use Analyze > Histogram to see which and how many pixels are depicted. You should also probably use a copy of your processed image prior to adding the LUT to compare to until you get used to reading the Histogram, but that shouldn't take long.
It may sound complicated at first but it isn't so don't get excited or discouraged as you go, I know you can do it.
Any other questions or problems then just let me know.
Bob
________________________________
From: Emily Teng <[hidden email]>
Sent: Tuesday, October 15, 2019 6:26 PM
To: [hidden email] <[hidden email]>
Subject: Re: Totally new here. Color Counter question
Dear Bob,
Thank you so much for your suggestions. Unfortunately, I am very ignorant on how to use the program. I don't know how to do most of you what you suggested. First:
Process > Image Expression Parser(Macro). Where is this? Something I need to add? I do know how to split the channels. ( Image > Color > Split Channels (make sure to keep the original)) but not how to use the parser macro to assign Red to A, Green to B, and Blue to C.
I guess the parser macro is where I am supposed to "Enter the equation in the field ,,,Sqrt(1-(A*A)/(B*B))?"
I see there are many LUTs but I don't know how to use them.
If you have the time and could give more detailed step by steps on how to do this, I would really appreciate it. I am learning, but have literally just downloaded the program a week ago and looked at a few tutorials so really know next to nothing....
Thank you so much.
Emily
--
ImageJ mailing list: https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7C%7C38c296a2c6e74bdaa05c08d751beba85%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637067751917071227&sdata=j77eEzO%2BNitHCuINJ3hzFOfGgqaMynf4i90yzvcfn9g%3D&reserved=0
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ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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