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Help with ImageJ please

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van der Merwe, Petrus

Help with ImageJ please

Good day sir/madam

I have downloaded, imagej and I believe that it is the tool I need.

I need to measure the density of wood in a stack, we know the stack is 50m long and 2m high and 2.4 m wide for instance, I want to take a picture of the stack from the side, like this one I have attached.

I want to run the measure function and get a value, hopefully percentage, that I can use to work out what the volume of wood in the stack is, if I have the percentage, I can say the stack is (50m x 2m x 2.4m) cubic meters, the percentage is 85 percent, so the volume is (50m x 2m x 2.4m) x 0.85 % , and work out the volume of the wood in this way,

Can imagej do this?, if else, can you put me onto someone who can help me, and tell me how to use imagej to calculate this.

Thanks a million.

PJ van der Merwe
LAN Administrator
Silicon Smelters (Pty) Ltd
Tel: +27 15 290 3129
Fax: +27 86 622 1782
E-Mail Address: [hidden email]
Postal address: Silicon Smelters (Pty) Ltd
Box 657
Polokwane
0700

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375915907_d8204f46c4.jpg (187K) Download Attachment

Tiago Ferreira-2

Re: Help with ImageJ please

On 2012.10.23, at 08:23 , van der Merwe, Petrus wrote:
>
> I need to measure the density of wood in a stack, we know the stack is 50m long and 2m high and 2.4 m wide for instance, I want to take a picture of the stack from the side, like this one I have attached.
> I want to run the measure function and get a value, hopefully percentage, that I can use to work out what the volume of wood in the stack i

There are multiple ways of achieving this. Here is one:

1) Convert the RGB image into an HSB stack using "Image>Type>HSB Stack"
(Check in the ImageJ user guide for a brief rational of why doing this conversion)

2) Scroll the new image stack using the bottom slider to the 3rd slice labeled "Brightness"

3) Open the threshold widget using "Image>Adjust>Threshold...". Tick the "Dark background"
checkbox and choose and appropriated threshold algorithm from the dropdown menu, such
as "Minimum"

4) Go to the "Analyze>Set measurements..." panel and tick the "Area fraction" checkbox.
This will give you the percentage of pixels in the image that are highlighted in red

5) Choose "Analyze>Measure" and note the value in the "%Area" column of the Results table

6) When analyzing multiple images use "Analyze>Summarize" to obtain group statistics

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

Rob van 't Hof-2

Re: Help with ImageJ please

In reply to this post by van der Merwe, Petrus

Hi Petrus,
Yes it can, and it is easiest done using a macro. I did a quick and
dirty one as an example:

//open your image file
open("");

//create a duplicate for processing
run("Duplicate...", "title=binary-in.jpg");

//convert duplicate to 8-bit grey scale
run("8-bit");

//filter out image noise
run("Median...", "radius=2");

//perform a threshold
setThreshold(65, 255);
run("Convert to Mask");

//close small gaps in thresholded image
run("Maximum...", "radius=2");
run("Minimum...", "radius=2");

//measure result
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00
show=Nothing clear summarize");

This was created using the macro recorder. very easy. The final result
is a summary iof the measurement including the percentage covered by "wood".

Hope this helps,

Rob

On 23/10/2012 13:23, van der Merwe, Petrus wrote:

> Good day sir/madam
>
> I have downloaded, imagej and I believe that it is the tool I need.
>
> I need to measure the density of wood in a stack, we know the stack is 50m long and 2m high and 2.4 m wide for instance, I want to take a picture of the stack from the side, like this one I have attached.
>
> I want to run the measure function and get a value, hopefully percentage, that I can use to work out what the volume of wood in the stack is, if I have the percentage, I can say the stack is (50m x 2m x 2.4m) cubic meters, the percentage is 85 percent, so the volume is (50m x 2m x 2.4m) x 0.85 % , and work out the volume of the wood in this way,
>
> Can imagej do this?, if else, can you put me onto someone who can help me, and tell me how to use imagej to calculate this.
>
> Thanks a million.
>
>
> PJ van der Merwe
> LAN Administrator
> Silicon Smelters (Pty) Ltd
> Tel: +27 15 290 3129
> Fax: +27 86 622 1782
> E-Mail Address: [hidden email]
> Postal address: Silicon Smelters (Pty) Ltd
> Box 657
> Polokwane
> 0700
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
_____________________________
Dr. Rob van 't Hof
Reader

Centre for Molecular Medicine
MRC IGMM
University of Edinburgh
Western General Hospital
Crewe Road, Edinburgh EH4 2XU
United Kingdom

Phone: (+44)-131-6511031
email: [hidden email]
_____________________________

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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

van der Merwe, Petrus

Re: Help with ImageJ please

Good day
Thanks a million, this works great, I will now have to do physical measurements in the field to test the ratio, to make sure that the values I get is within limits.

IMAGEJ is great

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Rob van 't Hof
Sent: 23 October 2012 18:45
To: [hidden email]
Subject: Re: Help with ImageJ please

Hi Petrus,
Yes it can, and it is easiest done using a macro. I did a quick and
dirty one as an example:

//open your image file
open("");

//create a duplicate for processing
run("Duplicate...", "title=binary-in.jpg");

//convert duplicate to 8-bit grey scale
run("8-bit");

//filter out image noise
run("Median...", "radius=2");

//perform a threshold
setThreshold(65, 255);
run("Convert to Mask");

//close small gaps in thresholded image
run("Maximum...", "radius=2");
run("Minimum...", "radius=2");

//measure result
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00
show=Nothing clear summarize");

This was created using the macro recorder. very easy. The final result
is a summary iof the measurement including the percentage covered by "wood".

Hope this helps,

Rob

On 23/10/2012 13:23, van der Merwe, Petrus wrote:

van der Merwe, Petrus

Re: Help with ImageJ please

In reply to this post by Tiago Ferreira-2

Good day

Thanks a million, I will definitely try this, I have been able to do it, thanks to the brilliant guys who have sent me tips.

Keep up the excellent work

regards

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Tiago Ferreira
Sent: 23 October 2012 16:59
To: [hidden email]
Subject: Re: Help with ImageJ please

On 2012.10.23, at 08:23 , van der Merwe, Petrus wrote:
>
> I need to measure the density of wood in a stack, we know the stack is 50m long and 2m high and 2.4 m wide for instance, I want to take a picture of the stack from the side, like this one I have attached.
> I want to run the measure function and get a value, hopefully percentage, that I can use to work out what the volume of wood in the stack i

There are multiple ways of achieving this. Here is one:

1) Convert the RGB image into an HSB stack using "Image>Type>HSB Stack"
(Check in the ImageJ user guide for a brief rational of why doing this conversion)

2) Scroll the new image stack using the bottom slider to the 3rd slice labeled "Brightness"

3) Open the threshold widget using "Image>Adjust>Threshold...". Tick the "Dark background"
checkbox and choose and appropriated threshold algorithm from the dropdown menu, such
as "Minimum"

4) Go to the "Analyze>Set measurements..." panel and tick the "Area fraction" checkbox.
This will give you the percentage of pixels in the image that are highlighted in red

5) Choose "Analyze>Measure" and note the value in the "%Area" column of the Results table

6) When analyzing multiple images use "Analyze>Summarize" to obtain group statistics

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

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