![]() ![]() On certain rare occasions, though, you make decisions In general, life is a big accumulation of small decisions youĭon't even think about. Northeastern University, but despite her age she was already doing great things To scikit-image who had made several incredibly technical pull requests, on myįavourite topic of extending n-dimensional support, and whom I'd thus asked The next week, at the Berkeley sprint, I finally met Kira Evans, a contributor In terms of speed, we knew it was doable, thanks to Martin Weigert's excellent minimal new windows and pop-ups, choosing layering instead.native (neither of us likes opening a browser to work).Loïc walking around San Francisco the weekend after I landed.įollowing on from his work on ClearVolume, Loïc and I agreed on some founding And so that evening, in Loïc'sĪpartment, napari (lowercase n) was born (though it did not yet have a name). Is so disparate between the two communities. Might well remain so, because the build, installation, and dependency tooling Scientific Python ecosystem, it remains challenging to use both together. Pushing the state of the art of deep learning in microscopy (and continues toĭo so), and, despite the hard work of many to integrate Fiji with the majorĭeep learning learning libraries (which are Python), as well as the wider ![]() So I was both shocked and delighted when Loïc casually mentioned that he neededĪ fast nD viewer in Python, and that we should build it together. Was I deluding myself that Python was important in Scikit-image, I've always been intimidated by Fiji and its ecosystem and itsġ0,000 15,000 citations. In fact,Īlthough I love Python and its ecosystem and what we've built with Microscope control library (you might detect a theme there ). Including ClearVolume, a super-fast 3D viewer, and ClearControl, a super-fast Java to me, and since then he'd worked on some incredible Java software, In Janelia he'd repeatedly extolled the virtues of Zuckerberg Biohub, so I asked him if I could crash at his place for a few days I'd recently seen thatįrom my Janelia days, had moved to San Francisco to start his lab at the Chan In May last year, Nelle Varoquaux organised a joint sprint withĭevelopers from scikit-learn, scikit-image, and dask at UC Berkeley, and I was In the meantime though, I was busy improving support for n-dimensional images I can't count the number of silly mistakes I made and dead ends IĬhased, just because I wasn't looking at the data enough. That I was looking at my data far less than I should have been, which slowedĭown my work. Python, with all the context switching that entailed. With either manually picking out 2D slices, or going back to tools outside of Given the lack of support, that 3D visualisation was not mission critical toĪnyone and not worth pursuing further. What's worse, I didn't see any movement on this - I even foundĪ very discouraging thread on MNE-Python in which Gaël Varoquaux concluded, Own orthogonal views viewer with Matplotlib (which was super slow), but nothing I tried a bunch of things after that time, including Mayavi and even building my Loading them into ITK-SNAP - which worked ok but required me to constantly beĬhanging terminals, and anyway was pretty inefficient because my disk ended up Using, or saving the volumes in VTK format and Quickly and it was a very smooth transition (highly recommended! ). I started out in Matlab, but moved to Python pretty Janelia Research Campus to work on the segmentation of 3D electron In 2009, I joined Mitya Chklovskii's lab and the FlyEM team at the I've been looking for a great nD volume viewer in Python for the better part ofĪ decade. It's still alpha software, but for months now, both theĬore napari team and a few collaborators/early adopters have been using napari We have been developing napari in the openįrom the very first commit, but we didn't want to make any premature fanfareĪbout it… Until now. I'm really excited to finally, officially, share a new(ish) project called ![]()
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