I am using ImageJ but it is not giving me clear images. I want to get crystal clear images free from the noise. I don't know how to use filters to increase the quality of my image. Can anyone please help on this?
Thanks
Hi Sarfaz,
I am sorry for just seeing this now. I am MIPAR's primary developer and appreciate Sayed's recommendation - it was a good one. Quite disappointed to see it down voted.
I have attached what MIPAR can do with your images. I have also attached the recipe files for each images's filtering. Just open the image in the Image Processor and load the corresponding recipe.
Gert's comments were very wise - you of course need to be careful when filtering images and be open about what you have done. But, as others have mentioned, filtering can be a useful means of discarding what our minds and experience know to be noise, such that the "principle components" of the image are better visualized and presented. One of MIPAR's nice features is the ability to "invert the filter" in the FFT filtering tool I used, to show exactly what image content has been removed.
I am here for any questions you have or help you need. If CRISP has not been doing what you need, or you need tools beyond just filtering, feel free to download MIPAR at http://mipar.us/trial.
Cheers,
John
As everything in life all is more complicated than it looks. If you scan literature you will find many images which perhaps looks bad but they simply cannot be improved because of inherently missing information. You can make them more "beautiful" but then you manipulate the original image which is against any ethic in science. An image shows what it shows. We are not working in advertisement where 60-years old people do not have any wrinkles.
On the other hand, working with software like WORD makes life easier but it doesn't write you an article. If you will get a car you are not automatically a racer even if it is racing car. You have to work with this software, you have to read about image processing and you need to understand what the software is doing. Who tells you that your "noise" is not a very important information? You interpret it as noise but it possibly contains more than you expect presently. And if it is noise, it tells you that your image collection was improper. You cannot replace the noise if there is no information.
By definition, every electron micrographs also contains noise. The noise can originate from the sample, contamination, imaging noise (several sources), and the shot noise of taking micrographs with electrons.
Your software can reduce some of that noise, but not all of it. In any case, as Gert mentioned, you will have to be very open on what you've done with your micrographs when you show / publish the results.
Now, your micrograph appears to be pretty high magnification and resolution. Which type of noise do you want to reduce? It is difficult to give detailed recommendations, if we don't know what you are shooting for....
Thanks everyone for the reply....Osama I will try MIPAR, thanks for this.... I am attaching one of the image from some thesis, he noise filtered the original image and that image has better atomic resolution than the original. I am also trying to improve the image quality of my TEM images but I coudnt. If some one has used imageJ with some kind of noise filter, that will be really helpful. thanks again...
Hi Sarfraz,
Now I know what you are looking for. You should try the little known program named "Crisp", which is produced and distributed by Sven Hovmoller's company Calidris in Sweden.
http://www.calidris-em.com
If you post the raw picture from your last figure here, I can give it a try since I still have Crisp installed on one of my old computers. That way you'll get to see what that little program can do.
Hi Wille,
Thanks for the help. CRISP seems good for my images. Do you know how to download CRISP? you can try this image.
Thanks
Hi Sarfraz,
My crusty old version of CRISP only handles pictures with fixed dimensions, e.g. 256x256, 512x512, etc.
Hence, I selected two 512x512 views from your micrographs. I'm showing the raw, unprocessed view, a high pass filtered view, and lattice filtered one. These were just "quick and dirty" processing attempts, with a bit more fiddling it should be possible to get (much) better results. Particularly, the lattice filtering would benefit from using even smaller windows within the 512x512 source image.
Now the bad news, this program is not available for free. You would have to contact the folks from Calidris to inquire about prices for a current version...
Cheers,
Holger
Hi Sarfaraz,
The image you showed from a thesis, seems to me an IFFT of the original image. You can get more nice looking images by IFFT but some reviewers do not trust IFFT images as you can get different images by applying different masks.
anyway, you can try Gatan DigitalMicrograph.
Cheers,
Ahmad
Hi Wille,
I don't know how to say thanks to you. lattice filtered images are very nice and I hope this will serve my purpose. I have already contacted these guys of calidris and I hope I will get this software.
Also Thanks Ahmad for the suggestion. Gatan software can be helpful but normally gatan products are very expensive, Any how I will first try with CRISP. Thanks Very much for giving such a useful reply.
Regards
Sarfraz
Hi Sarfaz,
I am sorry for just seeing this now. I am MIPAR's primary developer and appreciate Sayed's recommendation - it was a good one. Quite disappointed to see it down voted.
I have attached what MIPAR can do with your images. I have also attached the recipe files for each images's filtering. Just open the image in the Image Processor and load the corresponding recipe.
Gert's comments were very wise - you of course need to be careful when filtering images and be open about what you have done. But, as others have mentioned, filtering can be a useful means of discarding what our minds and experience know to be noise, such that the "principle components" of the image are better visualized and presented. One of MIPAR's nice features is the ability to "invert the filter" in the FFT filtering tool I used, to show exactly what image content has been removed.
I am here for any questions you have or help you need. If CRISP has not been doing what you need, or you need tools beyond just filtering, feel free to download MIPAR at http://mipar.us/trial.
Cheers,
John
Dear Sir,
If you have CRISP software , please provide the link. The link given in book "Electron Crystallography" by X. Zou, is not working .
Thanks
Hi Chandra,
The link I had provided two years ago (see above) still works.
Here it is again: http://www.calidris-em.com
Good luck
rather than quickly cleaning the image and making it more pleasing , keeping raw image provide more information. Some times cleaning image mislead other researchers working in the same field. I strongly support Gert Nolze argument, his words from his experience. So please think twice before you implement image processing on any microscopy image.
good luck ali
@ Caandra Bhal Singh
If you have Crisp download link can you share it with me, there is no download option at: http://www.calidris-em.com
It's not CRISP but you can try (or contact Zou):
https://www.mmk.su.se/zou/electron-crystallography-software
I am expert in biological sample preparation, ultra microtomy, operation of TEM and SEM with technical troubleshooting of TEM with more than 10 years experience from India’s largest public electron microscope facility.
Anyone have job for me?
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