http://imagej.273.s1.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5004208.html
AR in ImageJ is calculated as Major/Minor. I prefer the inverse as number ]0,1] instead of [1,…[ .
Concerning summary of AR and Round, I don't know. If they are set in "Set Measurements" they should appear as columns in the results table independent on mask treatment (run("Set Measurements…", "area centroid center perimeter bounding fit shape ferret's area_fraction display redirect=None decimal=3");). And hence would appear in the summary lines.
> Dear Karsten,
> I was having a look at the Shape descriptor values that I got for the
> images that I processed and found out that the value for Aspect Ratio was
> above 1. So in the particle summary Circ and Solidity were reported but not
> Aspect ratio and Roundness (Round). Is this because I did a bit of
> thresholding and water shed segmentation on the image or do you can you
> tell me the cause of these high values?
>
> Thank you
>
>
> On Sat, Jul 27, 2013 at 7:23 AM, Tola Ogunniyi <
[hidden email]> wrote:
>
>> Dear Karsten,
>> It was more of my Professor's choice for me to collect all the data
>> regardless of whether I need it or not, but I will focus on the ones you
>> have suggested for now. I thank you very much for responding on time and I
>> hope you have a great day.
>>
>>
>> On Sat, Jul 27, 2013 at 6:40 AM, Karsten Rodenacker-3 [via ImageJ] <
>>
[hidden email]> wrote:
>>
>>> Hi Geology Guy,
>>>
>>> Seemingly you have switched on all features. For the shape of particles
>>> there are IMHO only senseful:
>>>
>>> Area (*)
>>> Perimeter (*)
>>> Circ (*)
>>> Solidity (*)
>>> Round (*)
>>> Feret (*)
>>> MinFeret
>>> Minor/Major
>>>
>>> all others are related to redirection to gray scale image or not really
>>> helpful for particle shape description, better for representation e.g. by
>>> ellipsoids.
>>>
>>> To summarize a set of particles:
>>>
>>> The features (*) can be summarized by the usual Mean and SD.
>>>
>>> Min Feret is special, either the (global) Minimum or the span (Max-Min)
>>> could characterize the set os particles.
>>>
>>> Feret Angle and Angle might be helpful for elongated particles, but the
>>> mean of angles is a difficult task since angles come from a number module.
>>> (to difficult for the available time!)
>>>
>>> The mean of (Minor/Major), a ratio estimator is mean(Minor)/mean(Major)
>>> not mean(Minor/Major). SD of the ratio is a bit complicated too!
>>>
>>> I think this list of features should be enough for characterization of a
>>> set of particles!
>>>
>>> Hope that helps a bit
>>>
>>> Regards
>>> Karsten
>>>
>>> Am 27.07.2013 um 03:47 schrieb Geology Guy <[hidden email]<
http://user/SendEmail.jtp?type=node&node=5004175&i=0>>:
>>>
>>>
>>>> Dear Karsten,
>>>>
>>>> I am trying to measure the parameters of 100 particles in Image J and
>>> under
>>>> "Analyze Particles", I also selected the "Summary option". My main
>>> problem
>>>> now is that I deleted some of the particles as requested by my
>>> Professor
>>>> from the list after the data was provided by Image J. This makes the
>>>> "Summary" data not useful anymore as they do not reflect all the 100
>>>> particles I started with originally. I measured all the parameters
>>> under
>>>> "Set measurement" for each particle so now I need to produce a new
>>> summary
>>>> data as the values would be used in plotting graphs. I have figured out
>>> how
>>>> to Area which is just a simple addition of the areas of each particle.
>>>> Other parameters that are in the summary that I cannot determine from
>>> the
>>>> particles data are the following:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Perim.
>>>>
>>>> Major
>>>>
>>>> Minor
>>>>
>>>> Circ.
>>>>
>>>> Solidity
>>>>
>>>> Feret
>>>>
>>>> FeretX
>>>>
>>>> FeretY
>>>>
>>>> FeretAngle
>>>>
>>>> MinFeret
>>>>
>>>> IntDen
>>>>
>>>> Median
>>>>
>>>> Skew
>>>>
>>>> Kurt
>>>>
>>>>
>>>>
>>>> I have attached 2 Excel spreadsheets. The first shows my original
>>> particles
>>>> data and the highlighted rows in yellow are rows that I have deleted
>>> their
>>>> data as they are bad data. I am working on my research that is due on
>>> the
>>>> 31st of this month so this is very urgent. Thank you very much for your
>>>> assistance.
>>>>
>>>>
>>>> Yours faithfully,
>>>>
>>>> Tola
>>>>
>>>>
>>>> On Thu, Jul 4, 2013 at 5:10 PM, Karsten Rodenacker-3 [via ImageJ] <
>>>> [hidden email] <
http://user/SendEmail.jtp?type=node&node=5004175&i=1>>
>>> wrote:
>>>>
>>>>> Hi Geology Guy, possibly geologists think different.
>>>>>
>>>>> There are gray or color images with bright background and others with
>>> a
>>>>> dark background. This should not be mixed up with the representation
>>> of
>>>>> binary images. Foreground is always the set of pixels which are
>>> thresholded
>>>>> (shown with the small box) in the histogram of the interactive
>>> thresholding
>>>>> window. They get a value of 255. The background gets 0. Still by the
>>>>> Options->Colors… you can select the representation of foreground and
>>>>> background pixels.
>>>>>
>>>>> Maybe some clarification for you?
>>>>>
>>>>> Karsten
>>>>>
>>>>> (I have to confess that I rarely read manuals, I prefer trial and
>>> error)
>>>>>
>>>>> Am 04.07.2013 um 22:49 schrieb Geology Guy <[hidden email]<
>>>
http://user/SendEmail.jtp?type=node&node=5003767&i=0>>:
>>>>>
>>>>>
>>>>>> Dear Karsten,
>>>>>> Thanks for your response. I checked the Edit> Options> Colors and the
>>>>>> background is black while the Foreground is White. This is what I
>>> expect
>>>>>> because after reading the Image J manual, I learnt that Image J only
>>>>> makes
>>>>>> calculations from binary images when the background is black and the
>>>>>> foreground is white.
>>>>>>
>>>>>> I am using the default thresholding (i.e. AUTO) and checked the DARK
>>>>>> BACKGROUND BOX. Then when I was ready to do binary image a,dialogue
>>> box
>>>>>> popped up and I unchecked the box next to "BLACK FOREGROUND and WHITE
>>>>>> BACKGROUND". Again this setting that I am using is because the Image
>>> J
>>>>>> manual recommended a background that is black and white foreground in
>>>>> order
>>>>>> to be able to carry out calculations involving binary imaging. Or am
>>> I
>>>>> wrong
>>>>>> somewhere maybe that's why the background pixels are getting picked
>>> up
>>>>> in
>>>>>> the foreground when I try to calculate Area for foreground objects
>>> ONLY?
>>>>>> Thanks for your help.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> View this message in context:
>>>>>
>>>
http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003766.html>>>>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>>>>
>>>>>> --
>>>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>>>
>>>>> Karsten
>>>>> [hidden email] <
http://user/SendEmail.jtp?type=node&node=5003767&i=1>
>>>>>
>>>>> --
>>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>>>
>>>>>
>>>>> ------------------------------
>>>>> If you reply to this email, your message will be added to the
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>>>
http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003767.html>>>>> To unsubscribe from Isolating the background pixels from foreground
>>>>> pixels, click here<
>>>
>>>>> .
>>>>> NAML<
>>>
http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>>
>>>>>
>>>>
>>>>
>>>> W06.08_20 ParticleData.xls (50K) <
>>>
http://imagej.1557.x6.nabble.com/attachment/5004170/0/W06.08_20%20ParticleData.xls>
>>>
>>>> W06.08_20 Summary of Particle Data.xls (446 bytes) <
>>>
http://imagej.1557.x6.nabble.com/attachment/5004170/1/W06.08_20%20Summary%20of%20Particle%20Data.xls>
>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> View this message in context:
>>>
http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5004170.html>>>
>>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>>
>>>> --
>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>
>>> Karsten
>>> [hidden email] <
http://user/SendEmail.jtp?type=node&node=5004175&i=2>
>>>
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>>>
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>>> NAML<http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>>
>>
>>
>
>
>
>
> --
> View this message in context:
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>
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