Count intersection lines

[redcarnations]

i have membranes imaged. i want to put a straight line through the center of the image vertically and through the center horizontally and count how many times the straight lines intersects the membranes. i have tried thresholding the image and creating an outline but beyond this point, i am stuck. how do i make imagej count the number of times the straight lines intersect the membranes? is this even possible? thanks!

[Herbie-4]

Dear Noname,

your request is difficult to meet without seeing a typical image.

 From your description I'd try to analyze profiles along the desired
lines that of course must be line selections. How this 1D-analysis has
to be performed depends on the image...

Best

Herbie

:::::::::::::::::::::::::::::::::::::::
On 04.09.14 18:09, redcarnations wrote:

> i have membranes imaged. i want to put a straight line through the center of
> the image vertically and through the center horizontally and count how many
> times the straight lines intersects the membranes. i have tried thresholding
> the image and creating an outline but beyond this point, i am stuck. how do
> i make imagej count the number of times the straight lines intersect the
> membranes? is this even possible? thanks!
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Count-intersection-lines-tp5009504.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Mark Hiner]

Hi all,

 This question came up in the fiji-devel IRC channel today. The log and a
link to a partial solution can be found in the fiji-devel chat log
<http://code.imagej.net/chatlogs/fiji-devel?times=prefix&start-date=2014-09-04&start-time=0400&end-date=2014-09-05&end-time=0400>
.

Regards,
Mark


On Thu, Sep 4, 2014 at 12:03 PM, Herbie <[hidden email]> wrote:

> Dear Noname,
>
> your request is difficult to meet without seeing a typical image.
>
> From your description I'd try to analyze profiles along the desired lines
> that of course must be line selections. How this 1D-analysis has to be
> performed depends on the image...
>
> Best
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::
>
> On 04.09.14 18:09, redcarnations wrote:
>
>> i have membranes imaged. i want to put a straight line through the center
>> of
>> the image vertically and through the center horizontally and count how
>> many
>> times the straight lines intersects the membranes. i have tried
>> thresholding
>> the image and creating an outline but beyond this point, i am stuck. how
>> do
>> i make imagej count the number of times the straight lines intersect the
>> membranes? is this even possible? thanks!
>>
>>
>>
>> --
>> View this message in context: http://imagej.1557.x6.nabble.
>> com/Count-intersection-lines-tp5009504.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[redcarnations]

for example, an histology of lung alveoli.
if i wanted to see how many alveolar membranes the line intersected with

[Gabriel Landini]

On Friday 05 Sep 2014 18:30:59 you wrote:
> for example, an histology of lung alveoli.
> if i wanted to see how many alveolar membranes the line intersected with

I do not have the exact code, but here is an idea:
If the membranes are stained unequivocally, then take they profile of the
line. That profile should be bright where there is "air" and dark when it is a
stained membrane.
So counting the number of "regional minima" of at least a certain size (so you
do not get spurious ones) should be the number you are after.

Something like:
run("Tree Rings (48K)");
//setTool("line");
makeLine(929, 62, 1169, 64);
run("Plot Profile");

You get 9 regional minima. Since you can get the pixel values of the profile
into an array (there was a posting in the last few weeks exactly on this) then
you can compute the number of minima in the array.
You might also want to apply a running average to the array (or on the image)
to smooth out small perturbances (like the last one on the right generated
from the code above, which looks like a double valley.
Hope it helps.

Gabriel

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[Stoyan Pavlov]

Here's an idea:
Create a binary Image( with the same dimensions as your specimen
images) of your probing lines.
Next perform an Arithmetic "AND" with the image calculator between
line image and thresholded outline image. The resulting will contain
series of objects composed of the pixels where  the lines from the
first image intersect the outlines from. Count the objects and you
will have your count.
Stoyan
---
Dr. Stoyan P. Pavlov, MD, PhD
Departament of Anatomy, Histology and Embryology
Medical University "Prof. Dr. Paraskev Stoyanov", Varna
Prof. Marin Drinov Str.55
9002 Varna
 Bulgaria
Tel: +359 (0) 52 - 677 - 052
e-mail: [hidden email]
           [hidden email]


2014-09-06 11:40 GMT+03:00 Gabriel Landini <[hidden email]>:

> On Friday 05 Sep 2014 18:30:59 you wrote:
>> for example, an histology of lung alveoli.
>> if i wanted to see how many alveolar membranes the line intersected with
>
> I do not have the exact code, but here is an idea:
> If the membranes are stained unequivocally, then take they profile of the
> line. That profile should be bright where there is "air" and dark when it is a
> stained membrane.
> So counting the number of "regional minima" of at least a certain size (so you
> do not get spurious ones) should be the number you are after.
>
> Something like:
> run("Tree Rings (48K)");
> //setTool("line");
> makeLine(929, 62, 1169, 64);
> run("Plot Profile");
>
> You get 9 regional minima. Since you can get the pixel values of the profile
> into an array (there was a posting in the last few weeks exactly on this) then
> you can compute the number of minima in the array.
> You might also want to apply a running average to the array (or on the image)
> to smooth out small perturbances (like the last one on the right generated
> from the code above, which looks like a double valley.
> Hope it helps.
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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