Deconvolution Step-by-Step Guide with the Open Source BIPS on Linux and Windows
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- Опубликовано: 23 июл 2024
- Here I introduce the free and open source BiaQIm Image Processing Suite (BIPS) software.
I demonstrate how to install it and use it for blind and non-blind image deconvolution on both MS Windows and Linux. macOS users should also be able to use the software but I cannot demonstrate that since I do not have any Apple hardware.
CONTENTS
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00:00 Intro
01:03 Windows - installation and deconvolution tutorial
17:30 Linux - installation and deconvolution tutorial
27:39 Conclusions
SUPPORT PUMA
============
PUMA is an open source microscopy project. You can help support the project by:
1. Become a Patron: / pumamicroscope
2. Donate via PayPal: www.paypal.com/donate/?hosted...
3. Simply subscribing to this RUclips channel, like, comment and share these videos.
4. Spread the word - post the news about PUMA and link to this RUclips channel on your social media sites and any other outreach method (tell your friends, colleagues, students or teachers and lecturers about PUMA, for example).
5. Consider purchasing your optics and related supplies from our affiliated online optics store, OptArc.co.uk ( www.optarc.co.uk/ )
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LINKS REFERENCED IN THE VIDEO
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Get the free BIPS software (the only official download site):
www.optarc.co.uk/bialith/
More info and demos re deconvolution:
www.optarc.co.uk/deconvolve//...
OTHER LINKS
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PARD Capture software:
github.com/TadPath/PARDUS/tre...
PUMA Köhler Illuminator Specs document:
github.com/TadPath/PUMA/tree/...
FOR FURTHER INFORMATION
=======================
1. Open access write-up about PUMA on the FreeCAD blog:
blog.freecad.org/2023/02/13/a...
2. The official PUMA GitHub page where you can download the specs and source files to build or customise your own PUMA system:
github.com/TadPath/PUMA
3. The scientific peer reviewed publication on PUMA that was published in 2021 in the Journal of Microscopy (a journal of the Royal Microscopical Society) available here:
pubmed.ncbi.nlm.nih.gov/34151...
onlinelibrary.wiley.com/doi/1...
Thanks for your interest in the PUMA microscope system.
PJT 26/03/24 
Наука
For more background theory see my video on Convolution: ruclips.net/video/yF7-Crkuf7Y/видео.html
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Thanks.
After entering all the settings, when pressing "Start". I was getting an error: "path or file name not found". Reinstalling the program solved the problem
This is super cool. I'm a bit of a novice to these types of scientific image processing. For improving diffraction limited pictures on the PUMA microscope, would you prefer to use blind deconvolution? I'm guessing it might also be possible to try to use the spatial light modulator for SR-SIM or to determine the PSF using microparticles.
Thank you. I did a lot of work on super-resolution in bright field microscopy years ago and I hope to bring some of that to this channel over time. Yes - I hope also to demonstrate some SIM with PUMA - but there are a several more videos on the theory side I want to get out first so everyone can join the party.
@@PUMAMicroscope That sounds phenomenal! Thank you so much for continue to share your knowledge.
I have installed windows version and I try the example step by step according to your instructions, however when I press 'start' then after a few moments I get the following error:
a biaqlm header file cannot be found for the selected array/image.
Do you have any suggestion what could be the problem?
Thanks for the comment,. Clearly I can't know for sure but here are some possibilities / suggestions:
* One or more of the programs may not have installed correctly. Try a re-start of your computer. If that does not fix it, try uninstall and re-install +/- restart. Try typing the commands 'deconvolve' and 'fitsdou' (without any arguments) on a command window and see if they are recognised (you will get the standard usage message if it is recognised).
* It may be that some antivirus software has decided to block or quarantine some of the programs so you might need to look into that and re-install once permissions have been granted / files un-quarantined.
* All BIPS programs cannot handle any file name or directory path that contains spaces - so if you installed the program to something like 'My Programs' or if any of your files are in folders like 'My Document' (or anything with a space anywhere along the full path) then this could cause some programs to fail to find files and run.
* Check any feedback messages on the console window - these might give you a clue as to where the problem occurred or even what it is. If you are using the standard demo without alteration you should not require any additional dlls (if you tick the 'Use parallel' box then certain multithreading dlls will be required).
If you manage to get it working, consider making a reply to this comment to state what the problem was and how you fixed it to help others who have a similar issue.
Thanks,