bencardoen

DataCurator.jl

A scalable Julia package to transparently validate and transform large biomedical datasets using human readable recipes that are translated to machine verifiable templates.

smlmvis

Superresolution visualization of 3D protein localization data from a range of microscopes

singularity_slurm_cuda

Example on how to get started with Singularity and CUDA on a SLURM cluster

SPECHT.jl

SPECHT is a Julia implementation of a contrastive weakly supervised object detection and identification method for fluorescence microscopy.

singularity_julia

Template definition file for Singularity RO containers with Julia and user package embedded.

SubPrecisionContactDetection.jl

A Julia package to detect contacts below the precision of a superresolution microscope between 2 subcellular organelles in 2-channel superresolution (STED) microscopy.

bhattacharyya_distance

ERGO.jl

Object / density detection in astigmatic superresolution dSTORM microscopy

imaris_reader

paper_reviews

cedartutorial

Tips on how to leverage Compute Canada's HPC (Cedar) in your research.

clusim

An extended package for clustering similarity

Colocalization.jl

Colocalization metrics and distances for images or their sparse representations.

deep_loco

sample implementation of deeploco

ERGO

ERGO: Efficient Recurrent Graph Optimized Emitter Density Estimation in Single Molecule Localization Microscopy

ERGO.py

graph_course_presentation

julianotes

lab_tools

labtools

Set of utility scripts to ease remote mounting / ssh / data sync etc

launchjobs

Python script that runs arbitrary shell commands in parallel (for cluster/SLURM) usage

LogParadox.jl

Detects sufficient and necessary conditions for pattern inversion conditional on log transform

nbr

resources

Common resources used in scientific writing

sciparpy

SlurmMonitor.jl

A monitor for SLURM HPC schedulers that notifies on preset conditions (downtime, latency) and connects to Slack (optional)

SmlmTools.jl

Computational tools for single molecule localization / superresolution microscopy (point clouds).

srm_threshold

testccimac

testm1