Hello guys,
I am a beginner in microscopy and I need to analyse some data from live imaging from a spinning disk scope (BC43). I really like NIS-Elements AR software, where I anaysed some nd2 files as videos basically. You can really have all the feautures below the screen, like time, tiles, z-stacks and stop and run it as you like. Do you know if there is a similar software for BC43 (Andor) microscope? Preferably as open source, so I dont need to pay for a license.
Thanks a lot! Happy to hear your suggestions.
FYI: Software questions will see a broader range of subject matter experts over at forum.image.sc
Have you checked out Fiji/ImageJ? For highly complex datasets, like 3D tiles over time, it might not work as easily “out-of-the-box” as the instrument-specific software since those softwares are co-engineered with the file type. But for simple to moderately complex datasets it can be quite powerful. Since it is open source and costs you no money it often is not quote as user friendly as the commercial solutions, but it’s amazing once you get the hang of it. There’s a lot of online instructional material and forum.image.sc has loads of information and folks willing to help.
If you’re into coding, napari is a Python based package and they just launched a portal for ImageJ to expand capabilities. I have not used this myself so will rely on others to compare and contrast.
Hi there! Great, thank you very much for the information given! I have tried Fiji indeed. As you said it is nice but not so user friendly. But open source. Thank you as well for the forum.image.sc suggestion.
Yeah, there’s a reason the easy-to-use and powerful software packages cost a lot of money–making complex things easy to do takes a lot of work! There’s also a reason open-source software historically hasn’t been super user friendly–funding mechanisms paid for capability, but rarely UI. I’m so thankful for all the funding agencies that have started supporting all the great researchers continuing to work towards powerful and user-friendly open-source software.
As you may have experience from learning a new microscope, I often find that the second software package is actually the hardest/most frustrating to learn (many exceptions, of course). With the first, you don’t know what you’re doing and have to search for the answer, which is hard but also kind of fun. For the second, you know an answer but have to abandon that and start looking for the new one. It’s so tough! The hurdle that frustrates me the most in switching between software packages is that the same task often has different names in the different software. This then requires figuring out what each command is actually doing so you can find the equivalent command. So, while super frustrating, it often helps solidify the fundamentals. On the plus side, “translation” between software packages is something forum.image.sc or your local microscopy core facility staff can help with!
Good luck!
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Hey! Thank you very much for the insight and for sharing your experience in the field with me.
I am really beginner in all that, but seems very interesting. I can already tell that I “play” a lot with different microscopes and imaging analysis softwares.
Good luck to you too! And thank you once again!