schlegelp / nat.hdf5 Goto Github PK
View Code? Open in Web Editor NEWPlayground for reading neuron data from HDF into nat
License: GNU General Public License v3.0
Playground for reading neuron data from HDF into nat
License: GNU General Public License v3.0
@alexanderbates @jefferis: Moving the discussion on increase performance to GH.
As reminder, this was the most recent benchmark using ~1k hemibrain skeletons:
Reading from SWC (12Mb on disk): ~10s
Writing to RDS (4Mb on disk): 1s
Reading from RDS: <1s
Writing to Hdf5 (18Mb on disk): 50s
Reading from Hdf5: 20s
I just played with saving a string representing the serialised neuron alongside the other raw data.
In terms of writing data, this appears to add only ~10% to the time (50s->58s) but almost double the file size: 18Mb->33Mb.
For reading the file, that allows me to simply unserialise instead of creating the neurons from scratch which is obviously much faster: 20s->4s.
Note that this is all by making small changes to the existing read/write implementations and there might be additional mileage in refactoring. For example, I could serialise just the graph instead of the whole neuron - which I believe is the real bottleneck when re-creating a skeleton?
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.