Image capture for scientific processing in microscopy - an introduction

Introduction to the principles of scientific image capture for microscopy and astronomy. Choice of camera, reducing noise, flat-fielding, dark current correction, aliasing, Bayer artefacts, etc. CONTENTS ======== 00:08 Intro 00:43 Reasons for imaging 04:57 Setting up the scope and specimen 06:41 Choosing the right camera 10:06 Mounting the camera to the scope 10:50 Correcting for noise and artefacts 19:37 Conclusion SUPPORT PUMA ============ PUMA is an open source microscopy project. You can help support the project by: 1. Become a Patron: https://www.patreon.com/PUMAMicroscope 2. Donate via PayPal: https://www.paypal.com/donate/?hosted_button_id=NPMYJKJATDLQ4 3. Simply subscribing to this YouTube channel, like, comment and share these videos. 4. Spread the word - post the news about PUMA and link to this YouTube 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 ( https://www.optarc.co.uk/ ) --- LINKS ===== Online Poll (what would you like me to make a video on next?): https://www.youtube.com/post/UgkxHJBX5Z5aeHKD67s2JW6Svkus_ijaI_4J PARD Capture (free) software: https://github.com/TadPath/PARDUS/tree/main/PARD_Capture A user manual for the software is included in the User Manual for the OptArc.co.uk AF51 camera here: https://www.optarc.co.uk/support/ FURTHER READING ================ Dark field and Flat field correction http://spiff.rit.edu/classes/phys445/lectures/darkflat/darkflat.html https://core.ac.uk/download/pdf/37772805.pdf https://www.cfht.hawaii.edu/~baril/Pyxis/Help/flatdarkfield.html https://www.stsci.edu/instruments/wfpc2/Wfpc2_dhb/wfpc2_ch44.html http://astro.corlan.net/gcx/html/node7.html https://github.com/deepskystacker/DSS/releases/tag/4.2.2-Release Quantisation Errors Koeck, P. J. (2001). Quantization errors in averaged digitized data. Signal processing, 81(2), 345-356. Full paper available free here: https://www.researchgate.net/publication/220227127_Quantization_errors_in_averaged_digitized_data FOR FURTHER INFORMATION ======================= 1. Open access write-up about PUMA on the FreeCAD blog: https://blog.freecad.org/2023/02/13/a-research-grade-open-source-microscope-made-with-freecad/ 2. The official PUMA GitHub page where you can download the specs and source files to build or customise your own PUMA system: https://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: https://pubmed.ncbi.nlm.nih.gov/34151425/ https://onlinelibrary.wiley.com/doi/10.1111/jmi.13043