Re: HELP!!!-segmentation and quantification of DIC images
Posted by Robert Smith on Feb 27, 2020; 3:22pm
URL: http://imagej.273.s1.nabble.com/HELP-segmentation-and-quantification-of-DIC-images-tp5022977p5022978.html
Hello Dr. Zhang (you'll have to get used to it sooner or later),
The main problem is the angle of incidence of the light source being too steep. If illumination could be more normal to the surface and more evenly spread, it would be much better
ImageJ/Fiji is as good a software as any you will find to accomplish your goal.
Back to the illumination, because of the angle the droplets are highly illuminated on one side, and dark on the other leaving a terminator boundry between the two sides making a split . If you improve one side you decrease the other side and still maintain the split. The best option is to retake the images, diffuse the light and bring it more to the normal of the plane.
That being said, it can be done much better than I have here. I have included it only as an example as to what can be done.
Let us know if you will attempt again or just want to work with what you have.
Good Luck,
Bob
________________________________
From: Hui Zhang <[hidden email]>
Sent: Thursday, February 27, 2020 6:52 AM
To: [hidden email] <[hidden email]>
Subject: HELP!!!-segmentation and quantification of DIC images
<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.1557.x6.nabble.com%2Ffile%2Ft382540%2FDIC-droplets.png&data=02%7C01%7C%7Ced10770afbb14ef57ee208d7bb7e0a0f%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637184022309147093&sdata=pPYP6aCGdKotGIVWJNRrSmCI34GQ5W6ND570Qd6HQ6M%3D&reserved=0> Hi
I am a phD student in Germany. recently I am focusing on the phase
separation property of a protein.
As tested the GFP tag can enhance the ability of the protein to phase
sepatate, thus forming bigger droplets.
So I can only purified and utilize the untaged protein for assays and
generate a series of two dimentional DIC images with round shapes.
now the problem is that I need to quantify the number, size and roundess
(aspect ratio), which requires a good program to segmentate.
I attached an image also in case you want to have a look. you can see that
the background is not even, maybe it is not qualified, Do I need to generate
new images?
does someone of you know how to process or have some good program, software,
or plug-in that I can apply.
Best wishes
Hui Zhang
--
Sent from: https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.1557.x6.nabble.com%2F&data=02%7C01%7C%7Ced10770afbb14ef57ee208d7bb7e0a0f%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637184022309147093&sdata=K5BkLym4uyIz%2BZb4az%2BNkb6GM4ZmkgIfZcaj5n1SLAU%3D&reserved=0
--
ImageJ mailing list: https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7C%7Ced10770afbb14ef57ee208d7bb7e0a0f%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637184022309147093&sdata=QMKYbkgwjT1WWRIhJaGsq5m%2FzXNkRFxUZ6B%2BU4XhBD0%3D&reserved=0
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
URL: http://imagej.273.s1.nabble.com/HELP-segmentation-and-quantification-of-DIC-images-tp5022977p5022978.html
Hello Dr. Zhang (you'll have to get used to it sooner or later),
The main problem is the angle of incidence of the light source being too steep. If illumination could be more normal to the surface and more evenly spread, it would be much better
ImageJ/Fiji is as good a software as any you will find to accomplish your goal.
Back to the illumination, because of the angle the droplets are highly illuminated on one side, and dark on the other leaving a terminator boundry between the two sides making a split . If you improve one side you decrease the other side and still maintain the split. The best option is to retake the images, diffuse the light and bring it more to the normal of the plane.
That being said, it can be done much better than I have here. I have included it only as an example as to what can be done.
Let us know if you will attempt again or just want to work with what you have.
Good Luck,
Bob
________________________________
From: Hui Zhang <[hidden email]>
Sent: Thursday, February 27, 2020 6:52 AM
To: [hidden email] <[hidden email]>
Subject: HELP!!!-segmentation and quantification of DIC images
<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.1557.x6.nabble.com%2Ffile%2Ft382540%2FDIC-droplets.png&data=02%7C01%7C%7Ced10770afbb14ef57ee208d7bb7e0a0f%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637184022309147093&sdata=pPYP6aCGdKotGIVWJNRrSmCI34GQ5W6ND570Qd6HQ6M%3D&reserved=0> Hi
I am a phD student in Germany. recently I am focusing on the phase
separation property of a protein.
As tested the GFP tag can enhance the ability of the protein to phase
sepatate, thus forming bigger droplets.
So I can only purified and utilize the untaged protein for assays and
generate a series of two dimentional DIC images with round shapes.
now the problem is that I need to quantify the number, size and roundess
(aspect ratio), which requires a good program to segmentate.
I attached an image also in case you want to have a look. you can see that
the background is not even, maybe it is not qualified, Do I need to generate
new images?
does someone of you know how to process or have some good program, software,
or plug-in that I can apply.
Best wishes
Hui Zhang
--
Sent from: https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.1557.x6.nabble.com%2F&data=02%7C01%7C%7Ced10770afbb14ef57ee208d7bb7e0a0f%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637184022309147093&sdata=K5BkLym4uyIz%2BZb4az%2BNkb6GM4ZmkgIfZcaj5n1SLAU%3D&reserved=0
--
ImageJ mailing list: https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7C%7Ced10770afbb14ef57ee208d7bb7e0a0f%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637184022309147093&sdata=QMKYbkgwjT1WWRIhJaGsq5m%2FzXNkRFxUZ6B%2BU4XhBD0%3D&reserved=0
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Result of Result of fltr.png (4K) | Free forum by Nabble | Disable Popup Ads | Edit this page |