Integrated Pixel Density Units
Locked
Integrated Pixel Density Units
 
|
Dear Sir/Madam
I am having trouble establishing the units of integrated Pixel Density. So far I have analysed an 8-bit image with subtracted background and has a threshold of 0-255 of silver stained rat brain tissue. I know so far that pixel density is the sum of all the pixels in the given analysed area... But what are the units? When you get results summary, you get at 0.8 or 0.988 or 0.33 or even 1.23 - but in what? Many thanks, Hazel May -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Integrated Pixel Density Units
|
|
Hi Hazel,
The decimal numbers you gave take into account the spatial scaling (pixel size) of the image. For a strict sum of pixel intensities (without regard to spatial scaling) use the Raw Integrated Density (RawIntDen) value, which will be a whole number. To see/test this for yourself, change the scaling of an image (Image > Properties) to 1.0 x 1.0 pixels and your IntDen will match RawIntDen. If you change the pixel scaling to, for example, 0.1 x 0.1 microns your IntDen will be 1/100th of the RawIntDen value. To answer your original question, I guess the units of IntDen are 1/unit^2 (e.g. 1/micron^2). -Esteban On Jan 5, 2015 8:24 PM, "May, Hazel - (hazelmay)" < [hidden email]> wrote: > Dear Sir/Madam > > I am having trouble establishing the units of integrated Pixel Density. > So far I have analysed an 8-bit image with subtracted background and has a > threshold of 0-255 of silver stained rat brain tissue. > I know so far that pixel density is the sum of all the pixels in the given > analysed area... > But what are the units? When you get results summary, you get at 0.8 or > 0.988 or 0.33 or even 1.23 - but in what? > > Many thanks, > Hazel May > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Integrated Pixel Density Units
|
|
In reply to this post by May, Hazel - (hazelmay)
Hi Hazel,
These numbers may express the percentage of integrated intensity represented by any given region. Do you have something on the order of 100 regions in your image? The tutorial at: http://imagej.nih.gov/ij/docs/examples/dot-blot/ suggested this, which I found by looking at the Integrated Density entry at: http://rsbweb.nih.gov/ij/docs/guide/146-30.html I hope this helps. Michael On Mon, Jan 5, 2015 at 7:51 PM, May, Hazel - (hazelmay) < [hidden email]> wrote: > Dear Sir/Madam > > I am having trouble establishing the units of integrated Pixel Density. > So far I have analysed an 8-bit image with subtracted background and has a > threshold of 0-255 of silver stained rat brain tissue. > I know so far that pixel density is the sum of all the pixels in the given > analysed area... > But what are the units? When you get results summary, you get at 0.8 or > 0.988 or 0.33 or even 1.23 - but in what? > > Many thanks, > Hazel May > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Integrated Pixel Density Units
|
|
Thank you,
Another question however; my images were in inches as it appears. I have changed this to microns Now values are huge – due to the conversion obviously I also changed the scaled of the pixel width and height. To 1.0 and 0.1 microns and this alters my original values. If I were to graphy my results would and now I have gigantic numbers With inches and I have done analysis I get these results summary: Slice Count total area avg size %area mean IntDen 362686_30_RIGHT_PAAP_SILVER_20X-1.tif 16004 49.323 0.003 9.086 137.340 0.378 However in the results I get: Area mean StdDev Min Max IntDen %Area RawIntDen 16004 1.085E-4 144 0 144 144 0.016 100 144 Those are all when the images are in inches Now when I have them in Microns The Summary Slice Count total area avg size %area mean IntDen 362686_30_RIGHT_PAAP_SILVER_20X-1.tif 16004 47103308932.719 2943221.003 9.086 137.340 360729529.321 Results Area mean StdDev Min Max IntDen %Area RawIntDen 16004 103623.280 144 0 144 144 14921752.276 100 144 Im Struggling to interpret the results here I was told to take the IntDen from the summary and not the results…but they ‘re different numbers Plus I am not following the 1/unit^2 means.. Say unit being inches or microns. Is it a specific measurement of either unit? Sorry If I am asking basic questions or not being clear. I Just don’t know what I don’t know. Many Many Thanks Hazel -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Michael Sarahan Sent: Monday, January 05, 2015 9:57 PM To: [hidden email] Subject: Re: Integrated Pixel Density Units Hi Hazel, These numbers may express the percentage of integrated intensity represented by any given region. Do you have something on the order of 100 regions in your image? The tutorial at: http://imagej.nih.gov/ij/docs/examples/dot-blot/ suggested this, which I found by looking at the Integrated Density entry at: http://rsbweb.nih.gov/ij/docs/guide/146-30.html I hope this helps. Michael On Mon, Jan 5, 2015 at 7:51 PM, May, Hazel - (hazelmay) < [hidden email]> wrote: > Dear Sir/Madam > > I am having trouble establishing the units of integrated Pixel Density. > So far I have analysed an 8-bit image with subtracted background and > has a threshold of 0-255 of silver stained rat brain tissue. > I know so far that pixel density is the sum of all the pixels in the > given analysed area... > But what are the units? When you get results summary, you get at 0.8 > or > 0.988 or 0.33 or even 1.23 - but in what? > > Many thanks, > Hazel May > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Integrated Pixel Density Units
|
|
Hazel,
Your Min and Max are the same, are measuring a single pixel? -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of May, Hazel - (hazelmay) Sent: Tuesday, January 06, 2015 12:15 PM To: [hidden email] Subject: Re: Integrated Pixel Density Units Thank you, Another question however; my images were in inches as it appears. I have changed this to microns Now values are huge – due to the conversion obviously I also changed the scaled of the pixel width and height. To 1.0 and 0.1 microns and this alters my original values. If I were to graphy my results would and now I have gigantic numbers With inches and I have done analysis I get these results summary: Slice Count total area avg size %area mean IntDen 362686_30_RIGHT_PAAP_SILVER_20X-1.tif 16004 49.323 0.003 9.086 137.340 0.378 However in the results I get: Area mean StdDev Min Max IntDen %Area RawIntDen 16004 1.085E-4 144 0 144 144 0.016 100 144 Those are all when the images are in inches Now when I have them in Microns The Summary Slice Count total area avg size %area mean IntDen 362686_30_RIGHT_PAAP_SILVER_20X-1.tif 16004 47103308932.719 2943221.003 9.086 137.340 360729529.321 Results Area mean StdDev Min Max IntDen %Area RawIntDen 16004 103623.280 144 0 144 144 14921752.276 100 144 Im Struggling to interpret the results here I was told to take the IntDen from the summary and not the results…but they ‘re different numbers Plus I am not following the 1/unit^2 means.. Say unit being inches or microns. Is it a specific measurement of either unit? Sorry If I am asking basic questions or not being clear. I Just don’t know what I don’t know. Many Many Thanks Hazel -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Michael Sarahan Sent: Monday, January 05, 2015 9:57 PM To: [hidden email] Subject: Re: Integrated Pixel Density Units Hi Hazel, These numbers may express the percentage of integrated intensity represented by any given region. Do you have something on the order of 100 regions in your image? The tutorial at: http://imagej.nih.gov/ij/docs/examples/dot-blot/ suggested this, which I found by looking at the Integrated Density entry at: http://rsbweb.nih.gov/ij/docs/guide/146-30.html I hope this helps. Michael On Mon, Jan 5, 2015 at 7:51 PM, May, Hazel - (hazelmay) < [hidden email]> wrote: > Dear Sir/Madam > > I am having trouble establishing the units of integrated Pixel Density. > So far I have analysed an 8-bit image with subtracted background and > has a threshold of 0-255 of silver stained rat brain tissue. > I know so far that pixel density is the sum of all the pixels in the > given analysed area... > But what are the units? When you get results summary, you get at 0.8 > or > 0.988 or 0.33 or even 1.23 - but in what? > > Many thanks, > Hazel May > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Integrated Pixel Density Units
|
|
No it’s a un-selected area where the images are binary and show numerous black dots as it was stained with Silver
From what I know, I'm not.. -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of MODEL, MICHAEL Sent: Tuesday, January 06, 2015 11:03 AM To: [hidden email] Subject: Re: Integrated Pixel Density Units Hazel, Your Min and Max are the same, are measuring a single pixel? -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of May, Hazel - (hazelmay) Sent: Tuesday, January 06, 2015 12:15 PM To: [hidden email] Subject: Re: Integrated Pixel Density Units Thank you, Another question however; my images were in inches as it appears. I have changed this to microns Now values are huge – due to the conversion obviously I also changed the scaled of the pixel width and height. To 1.0 and 0.1 microns and this alters my original values. If I were to graphy my results would and now I have gigantic numbers With inches and I have done analysis I get these results summary: Slice Count total area avg size %area mean IntDen 362686_30_RIGHT_PAAP_SILVER_20X-1.tif 16004 49.323 0.003 9.086 137.340 0.378 However in the results I get: Area mean StdDev Min Max IntDen %Area RawIntDen 16004 1.085E-4 144 0 144 144 0.016 100 144 Those are all when the images are in inches Now when I have them in Microns The Summary Slice Count total area avg size %area mean IntDen 362686_30_RIGHT_PAAP_SILVER_20X-1.tif 16004 47103308932.719 2943221.003 9.086 137.340 360729529.321 Results Area mean StdDev Min Max IntDen %Area RawIntDen 16004 103623.280 144 0 144 144 14921752.276 100 144 Im Struggling to interpret the results here I was told to take the IntDen from the summary and not the results…but they ‘re different numbers Plus I am not following the 1/unit^2 means.. Say unit being inches or microns. Is it a specific measurement of either unit? Sorry If I am asking basic questions or not being clear. I Just don’t know what I don’t know. Many Many Thanks Hazel -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Michael Sarahan Sent: Monday, January 05, 2015 9:57 PM To: [hidden email] Subject: Re: Integrated Pixel Density Units Hi Hazel, These numbers may express the percentage of integrated intensity represented by any given region. Do you have something on the order of 100 regions in your image? The tutorial at: http://imagej.nih.gov/ij/docs/examples/dot-blot/ suggested this, which I found by looking at the Integrated Density entry at: http://rsbweb.nih.gov/ij/docs/guide/146-30.html I hope this helps. Michael On Mon, Jan 5, 2015 at 7:51 PM, May, Hazel - (hazelmay) < [hidden email]> wrote: > Dear Sir/Madam > > I am having trouble establishing the units of integrated Pixel Density. > So far I have analysed an 8-bit image with subtracted background and > has a threshold of 0-255 of silver stained rat brain tissue. > I know so far that pixel density is the sum of all the pixels in the > given analysed area... > But what are the units? When you get results summary, you get at 0.8 > or > 0.988 or 0.33 or even 1.23 - but in what? > > Many thanks, > Hazel May > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
«
Return to ImageJ
|
1 view|%1 views
| Free forum by Nabble | Edit this page |