I advise you to go to Dr. Jacek Wierzchos, highly skilled

As with other microscopes, the rule is: The better images (lower noise and background, higher contrast), the easier analysis. With some types of images thresholding simply does not work. With SIM there is an additional problem of image reconstruction artifacts (ringing, high noise, false structures) when you push the resolution too high.

If you post a sample image somewhere, someone might be able to suggest the right segmentation method.

Hello ...I have worked with that kind of images... sometimes the illumination is parabolic... so, it has to be corrected. I wrote a paper with my approach. Best regards!. https://www.academia.edu/956732/Correcci%C3%B3n_Alineaci%C3%B3n_y_Reconstrucci%C3%B3n_3D_a_partir_de_Cortes_Seriados_Un_Caso_de_Estudio

Hi Zdenek,

I have attached an example images. I guess, I am aware of the problems you mentioned above and have kind of passed those hurdles. Now have to find a way o analyse them. 

Best Regards

Sushma

Hello Rhadames,

Thanks for the link, but it seems to be in Spanish.

Best

Sushma

Hi Carmen,

Thanks for the suggestion. I appologies for my lack of awareness but I was wondering if Dr. Jacek Wierzchos works on SIM or Synapse related structures.

Best

Sushma

Dear Sushma, in RE to your saying above:    "I have attached...."

just to tell you that during my access of the thread/Question I only found a small rectangle - when clicking there:  I got an automatic reply in a new small icon telling:

I am not quite sure what others will have ...

It might be that your .TIF either wasn't loaded properly or TIF's aren't allowed in RG to be downloaded(?).

Perhaps (and if you don't mind)  you transform your  .tif to a  .jpg-file and try again to download to the thread.

Thank you,

best wishes and regards.

Dear Wolfgang,

I am sorry, I did not realize that aatchement did not work.  I am also not sure of the reason but have attached the jpg file and it works.

Thanks

Sushma

Dear Sushma, thank you !

Best wishes and regards, Wolfgang

Hi Sushma have you tried older versions of fiji they have good background correction functions: sliding paraboloid, or colour separation, or rolling ball, etc

Also maybe "find maxima" can help, in worst case contact the imageJ list on IMAGEJ /at/  LIST.NIH.GOV

good luck!!

Hi Toufic,

I had not tried older version of fiji. Thanks for the suggestion. I will look for it.

Thanks

Sushma

hello!

Are you trying to reconstruct 9 or 15 raw images captured by SIM camera to a super-resolution image? I'm also working with this problem. Do you have any progress? You can go to Dr. Guy_Hagen

Hi Sushma,

Could you be more specific of your problem or what you want to analyze?

Best,

Bo-Jui

Hi Luo,

Yes, I am doing Z stack imaging and then take the maximum intensity projection(MIP) for the analysis. Actually, I wanted to find an automated method to threshold the image before measuring the area for PSD-95. But none of the available method worked for me. So for now, I am doing manual thresholding.

Did you found some solution?

Best

Sushma

Hi Bo-Jui,

I want to analyze the size of pre and post synaptic markers using SIM microscopy. I could get the nice images but have not find any automated method for thresholding.

Any suggestions?

Best

Sushma