Query regarding image processing

[Igor Makarovsky]

Dear All,

My name is Igor and I work for a Pharma company. I have a series of SEM images, from which I have to calculate the relative percentage of the Nano-sized particles. You can see a sample of such an image attached. I know what I want to do - to scale the whole image and subtract the big lumps, but I don't exactly know how to do it. Please advise me how to go about it.

Thank you all in advance,
Best Regards,
Igor


[cid:image001.png@01D6A553.2A2BF200]


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[Herbie]

Greetings Igor,

not sure if I can read your mind and "know what [you] want to do".

First let me state that I doubt that the provided sample image is an
original image from your EM. The bottom legend is oblique...

Please tell us why you have this enormous gradient in the image which is
detrimental for image analyses.

Furthermore, please stay away from lossy image compression, i.e.
JPG-format. Please provide high quality images in the original
uncompressed data format such as PNG or TIFF.

Please describe more detailed what you regard as "big lumps" and what
you call nano-sized particles.

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::
Am 18.10.20 um 12:33 schrieb Igor Makarovsky:
> Dear All,
>
> My name is Igor and I work for a Pharma company. I have a series of SEM images, from which I have to calculate the relative percentage of the Nano-sized particles. You can see a sample of such an image attached. I know what I want to do - to scale the whole image and subtract the big lumps, but I don't exactly know how to do it. Please advise me how to go about it.
>
> Thank you all in advance,
> Best Regards,
> Igor

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[Gabriel Landini]

On Sunday, 18 October 2020 11:33:00 BST [hidden email] wrote:
> I have a series of SEM
> images, from which I have to calculate the relative percentage of the
> Nano-sized particles.

If the scale bar (10 micrometres) is correct, I am afraid that you cannot
image nanoparticles at that magnification. Nanoparticles are normally defined
as having between 1 and 100 nanometres in diameter, not micrometres!

Cheers

Gabriel

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[Igor Makarovsky-2]

Dear Gabriel,
I tried to send the original image, but it was too big to send (5.76 MB)
and not 4M that the nih mail restricted. So I photographed the image and
sent it for your appreciation. Please find the original image attached via
wetransfer (https://we.tl/t-Td7yO8gKSI). What I need to do is to determine
the percentage of the nano-sized particles in the image. I deliberately
chose this particular image because you can see both sizes. The bigger
lumps are the micro particles or clusters of nano-sized particles
aglomerated together and the background is laced with nano particles
(please find another image - a higher magnification). I thought doing area
fraction calculation, but not sure this is the right technique, because the
bigger lumps are also covered in these nano needles.

Thank you for your help,
Igor

On Sun, 18 Oct 2020 at 15:20, Gabriel Landini <[hidden email]> wrote:

> On Sunday, 18 October 2020 11:33:00 BST [hidden email] wrote:
> > I have a series of SEM
> > images, from which I have to calculate the relative percentage of the
> > Nano-sized particles.
>
> If the scale bar (10 micrometres) is correct, I am afraid that you cannot
> image nanoparticles at that magnification. Nanoparticles are normally
> defined
> as having between 1 and 100 nanometres in diameter, not micrometres!
>
> Cheers
>
> Gabriel
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Igor Makarovsky, Ph.D.
Head Formulator

Tree of Life Pharma Ltd.
1 Bat-Sheva st., POB 799
Lod 7110604, Israel

Phone [phone]
Mobile [phone]
Fax [phone]

e-mail: [hidden email]
<https://xmail.weizmann.ac.il/ecp/Customize/gmail.com> or [hidden email]
<[hidden email]>o.il

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[Herbie]

Igor,

attached please find the result of some pre-processing of a top right
square area of your sample image "sample 1 2".

It appears near to impossible to find an adequate thresholding scheme
that reflects a reasonable foreground / background relation, i.e. the
desired coverage.
(Using the "Default"-scheme I get a coverage in the investigated area of
about 50%.)

I still have problems interpreting sample image "sample 1 16" that shows
no detectable relation to sample image "sample 1 2".

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::
Am 18.10.20 um 14:58 schrieb Igor Makarovsky:

> Dear Gabriel,
> I tried to send the original image, but it was too big to send (5.76 MB)
> and not 4M that the nih mail restricted. So I photographed the image and
> sent it for your appreciation. Please find the original image attached via
> wetransfer (https://we.tl/t-Td7yO8gKSI). What I need to do is to determine
> the percentage of the nano-sized particles in the image. I deliberately
> chose this particular image because you can see both sizes. The bigger
> lumps are the micro particles or clusters of nano-sized particles
> aglomerated together and the background is laced with nano particles
> (please find another image - a higher magnification). I thought doing area
> fraction calculation, but not sure this is the right technique, because the
> bigger lumps are also covered in these nano needles.
>
> Thank you for your help,
> Igor
>
> On Sun, 18 Oct 2020 at 15:20, Gabriel Landini <[hidden email]> wrote:
>
>> On Sunday, 18 October 2020 11:33:00 BST [hidden email] wrote:
>>> I have a series of SEM
>>> images, from which I have to calculate the relative percentage of the
>>> Nano-sized particles.
>>
>> If the scale bar (10 micrometres) is correct, I am afraid that you cannot
>> image nanoparticles at that magnification. Nanoparticles are normally
>> defined
>> as having between 1 and 100 nanometres in diameter, not micrometres!
>>
>> Cheers
>>
>> Gabriel

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