WhoIsJack
Systems biologist studying the principles of self-organization at the interface of cell and developmental biology.
University College LondonLondon, United Kingdom
WhoIsJack's Stars
cxli233/FriendsDontLetFriends
Friends don't let friends make certain types of data visualization - What are they and why are they bad.
python-adaptive/adaptive
:chart_with_upwards_trend: Adaptive: parallel active learning of mathematical functions
google/neuroglancer
WebGL-based viewer for volumetric data
neka-nat/probreg
Python package for point cloud registration using probabilistic model (Coherent Point Drift, GMMReg, SVR, GMMTree, FilterReg, Bayesian CPD)
cgohlke/tifffile
Read and write TIFF files
DedalusProject/dedalus
A flexible framework for solving PDEs with modern spectral methods.
SHTOOLS/SHTOOLS
SHTOOLS - Spherical Harmonic Tools
scverse/spatialdata
An open and interoperable data framework for spatial omics data
pysb/pysb
Python framework for Systems Biology modeling
CiwPython/Ciw
Ciw is a simulation library for open queueing networks.
dpeerlab/spectra
Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
pyxu-org/pyxu
Modular and scalable computational imaging in Python with GPU/out-of-core computing.
AMICI-dev/AMICI
Advanced Multilanguage Interface to CVODES and IDAS
quadbio/Pando
Multiome GRN inference.
sys-bio/tellurium
Python Environment for Modeling and Simulating Biological Systems
cdelker/schemdraw
multiview-stitcher/multiview-stitcher
A toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.
m-albert/MVRegFus
Python module for registering and fusing multi-view microscopy data
VasylVaskivskyi/microaligner
Image registration (alignment) software for large microscopy images
DanuserLab/u-unwrap3D
Transform 3D cell surfaces into different representations including topographic maps, 3D spheres, and 2D images for doing optimized quantification, data analysis and machine learning.
morphometrics/morphometrics
GrotjahnLab/surface_morphometrics
Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging.
maxschelski/figureflow
Fast, modular and reproducible generation of publication quality scientific figures and movies with only a few lines of code.
VirtualEmbryo/foambryo
Python package to infer tensions and pressures from 3D microscopy images of embryos and tissues
DeVriesMatt/cellshape
3D shape analysis of cancer cells using deep learning
applied-systems-biology/Dynamic_SPHARM
Software for dynamic spherical harmonic analysis
DanuserLab/u-signal3D
The computational platform u-signal3D defines a shape-invariant representation of the spatial scales of molecular organization at the cell surface, enabling comparison and machine-learning of signaling across morphologically diverse cell populations.
VirtualEmbryo/delaunay-watershed
Python package to reconstruct a multimaterial nonmanifold surface mesh from 3D segmentation masks of tissues or nuclei
WhoIsJack/tissue_exploder
Create a nice exploded visualization of segmented cells in a tissue.
raible-lab/neuromast3d
Code for the 3d neuromast cell and nuclear shape project