habi

Working dad, born at 333 ppm. Generic geek and ex-messenger with a PhD in ultrahigh resolution tomography. I love the outdoors, my bikes, swimming & much more.

Institute of Anatomy, Unversity of Bern, SwitzerlandBern, Switzerland

Pinned Repositories

acinar-analysis-manuscript
Language:HTML2 3 80
EAWAG-manuscript
A small manuscript on the preparation and tomographic scanning of a corpus of cichlids from the EAWAG. And a bit on the treatment of the data.
Language:HTML2 2 115
GlobalDiagnostiX
Code and stuff written for my work on http://globaldiagnostix.org/
Language:Python21 9 819
latex
Some LaTeX code snippets I've hacked together over the years.
Language:TeX138 12 245
latex-test
Results (automatically) in http://habi.github.io/latex-test/main.pdf
Language:TeX8 2 18
Lecture.Microtomography
A lecture on (micro)tomography
Language:TeX3 2 70
OpenSCAD
A collection of OpenSCAD models; stuff to fix private 'issues' and gifts
Language:OpenSCAD8 3 03
PhD-Thesis
My PhD-Thesis, copied from the virtual SVN-server I installed at the Institute of Anatomy of the University of Bern in Switzerland and migrated to git.
Language:TeX24 3 05
Zebra-Fish-Gills
Analysis for https://doi.org/10.1371/journal.pone.0228333
Language:Jupyter Notebook3 4 51
zmk-tooth-cohort
Scanning +100 teeth with our sample changer
Language:Jupyter Notebook3 2 22

habi's Repositories

habi/latex
Some LaTeX code snippets I've hacked together over the years.
Language:TeX138 12 245
habi/Lecture.Microtomography
A lecture on (micro)tomography
Language:TeX3 2 70
habi/catalog
Made with Manubot catalog (please add your manuscript!!)
Language:Python1 1 0
habi/heart-neoangiogenesis
Analyzing tomographic scans of rat hearts
Language:Jupyter Notebook1 2 0
habi/name-suggestion-index
Canonical common brand names, operators, transit and flags for OpenStreetMap.
Language:JavaScript1 0 0
habi/wilkerstrasse.ch
Website für die Wilkerstrasse
Language:HTML1 3 0
habi/aare_meter
Retro thermometer of the river Aare, realized with an ESP32 and a voltmeter
habi/blog
My blog. Ran under http://habi.gna.ch with WordPress, is now also available http://blog.davidhaberthuer.ch, run by `hugo`
Language:Hack3 10
habi/BrukerSkyScanLogfileRuminator
Boilerplate code to work with logfiles of tomograpic data acquired with Bruker SkyScan machines
Language:Jupyter Notebook2 0
habi/CryoVesNet
segmentation of spherical vesicles in cryo-electron tomography
habi/dask-image
Distributed image processing
habi/dotfiles
Tracking the settings of my most-used linux utilities.
Language:Shell2 1
habi/E461
E461 is Methyl cellulose and has a wide range of uses. Working on tomographic data of Methyl cellolose foams with a team of the Berner Fachhochschule, Hochschule der Künste Bern, Konservierung und Restaurierung
Language:Jupyter Notebook1 0
habi/FemalePelvicFloor
Files/Data to work on the female pelvic floor project
Language:Jupyter Notebook2 0
habi/fotoalign
Language:Jupyter Notebook
habi/graiz
Public Bio
habi/imagej.github.io
The ImageJ wiki
Language:JavaScript0 0
habi/InMiceMethodPaper
Language:HTML3
habi/Laminitis
Language:Jupyter Notebook1 01
habi/meta-cli
tomo-meta contains meta-data readers for laboratory and synchrotron based tomography instruments
habi/obi
habi/osm-admin-boundary-conflation
Language:Python1 0
habi/osm-community-index
:speech_balloon: An index of community resources for OpenStreetMap
Language:JavaScript0 0
habi/pinboard-angelesen
A simple aggregator for my weekly posts. Consumes a feed from pinboard.in and exports them as markdown
Language:PHP2 0
habi/porespy
A set of tools for characterizing and analying 3D images of porous materials
Language:Python0 0
habi/pystack3d
Package to process images stacks (typically from 3D FIB-SEM)
habi/rootstock
Clone me to create your Manubot manuscript
Language:HTML0 0
habi/sticklebacks
Datwrangling tomographic scans of sticklebacks
Language:Jupyter Notebook2 0
habi/switch2osm
habi/Talk.2025.COMULIS
Language:TeX