JuliaMicroscopy org?

I was curious about possibly starting a JuliaMicroscopy org for microscopy-specific packages. I have some research code I’ve published, and MATLAB code I’m interested in porting to Julia. @nboyd also has a localization microscopy-related packages (Interest in single molecule localization microscopy? - #2 by tim.holy), and there’s a package for OME-TIFFs over here: Package for working with OMETIFF files in Julia! - Announcements - Image.sc Forum

How does one do that?


I think that anyone can create an organization on GitHub; then you just add teams/contributors and packages. The hard part is the social one, getting folks to contribute their packages. But orgs have worked out pretty well in general, so I think it might be merited.



potentially @RainerHeintzmann is also interested.

We currently work on several packages like DeconvOptim.jl, FourierTools.jl, PSFs.jl, View5D.jl, etc which all more or less target microscopy.

I’m also going to start my PhD soon and plan to work (almost) exclusively with Julia.

So yeah, might make sense to found one and then we can start moving packages slowly?


Sounds like a good idea. As Felix wrote, we are currently active creating a few tools for microscopy use in Julia. In addition to Felix’s list, PSFs.jl is also coming up. To collect useful packages under one heading seems good to me.


It’s been created! JuliaMicroscopy · GitHub

I also sent invites.


I’m in. Is this when we start thinking about a Julia themed logo?

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My vote for image


@cormullion :point_up: There is a new Julia org that needs a nice logo. I thought that designing a “Julia microscope” could be a nice challenge for you :grinning_face_with_smiling_eyes:

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Hmm I don’t think an old-timey microscope would be that easy - but if I remember rightly what looking through one was like, it’s kind of like this?

Screenshot 2021-08-24 at 15.33.02

but this is probably “floppy disk icon means ‘save’” level of icongraphy :rofl:


My thought would be a series of lenses in the Julia colors:


A nice idea!

If you wanted more realistic-looking optics, perhaps Makie could do something, although for icons it’ s usually better to stay abstract…


It might be also worth to think about using the JuliaOptics Org (which has been used it the past and has currently different ownership) instead of focusing too much on microscopy?


Nice! One bit of realism it’d be good to add, if possible, is the light rays bending at the surfaces of the lenses, rather than their centers.


Could use a configuration of lenses more typical of microscope objectives, for example:

Well you learn something every day, :slight_smile: Wouldn’t be too difficult.

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I hear you. :slight_smile: Maybe this is getting into the weeds, but I think the green lens should be concave, in order to turn converging rays into parallel, kind of an inversion of the first, purple, lens. Probably best to run it by an optics exert to make sure it all makes sense.


As usually there is a conflict between being technically precise and having an expressive graphical design. Real compound lens are never symmetric, I beleive (I’m not an optics expert), and nowadays pretty complex (see the post by BioTurboNick above), whereas the logo should preferably be simple enough and somehow symmetric (I’m even less a graphics expert).

Maybe something like this? That wouldn’t be completely physically wrong, and simple enough. Note different curvature of the inner interfaces vs. outer surfaces.

A “real world” note - in lens design, interfaces glas/air are to be avoided as much as possible due to light reflection from the interface.


googling for “compound lens” images brought about less than I hoped for, but here you may find some ideas:

X Line Objectives Offer Revolutionary Optical Performance Thanks to Advanced Manufacturing Technology | Olympus LS (Fig. 5-6, 5-7)

Optical lens definition - Photokonnexion ( Compound optical lenses)

Definitions of Photography Terms (APO)

I’m in if only to represent the entomology crowd. I have some measurement projects that could really use Julia’s help

Personally like the logo by @cormullion but what happened to the blue dot over the “J” in Julia?

Now where did I leave that net…

I’m looking forward to PSFs.jl! Actually I have a (non-polished) PSF calculator in Julia as well… Looking forward to comparing and maybe contributing.