TorecLuik
Working on Machine Learning, Software Development, Software Architecture and DevOps at the Core Facility for Cellular Imaging of the Amsterdam UMC, location AMC
Core facility - Cellular Imaging, Amsterdam UMC @NL-BioImaging Amsterdam
Pinned Repositories
biomero
BIOMERO - A python library for easy connecting between OMERO (jobs) and a Slurm cluster
slurm-scripts
Scripts for running on SLURM
Biaflows-bootstrap
Biaflows installation procedure on a web server or a personal laptop. This procedure is based on ULiege Cytomine bootstrap (see @cytomine-uliege & @cytomine).
biaflows-utilities
Python library containing utility functions used within BIAFLOWS wrapper files (annotation export, metrics computation).
biaflows_jupyter_local
A jupyter-notebook that demonstrates the local use of BIAFLOWS, with SLURM
cytomine-utils
Util scripts for Cytomine
docker-from-omero-poc
proof-of-concept running docker container from omero web
omero-guide-python
More omero scripts
omero-py
Python project containing Ice remoting code for OMERO
TorecLuik's Repositories
TorecLuik/W_NucleiSegmentation-Cellpose
TorecLuik/W_NucleiSegmentation-CellProfiler
NEUBIAS-WG5 workflow for nuclei segmentation using CellProfiler 2.2.0
TorecLuik/biaflows-utilities
Python library containing utility functions used within BIAFLOWS wrapper files (annotation export, metrics computation).
TorecLuik/W_SpotCounting-CellProfiler
TorecLuik/slurm-scripts
Scripts for running on SLURM
TorecLuik/W_CountMaskOverlap
Counting granules in cells. Provide input in 1 directory with suffixes on pairs of masks.
TorecLuik/W_CellExpansion
CellExpansion
TorecLuik/packaging_tutorial
TorecLuik/omero-guide-python
More omero scripts
TorecLuik/cytomine-utils
Util scripts for Cytomine
TorecLuik/Biaflows-bootstrap
Biaflows installation procedure on a web server or a personal laptop. This procedure is based on ULiege Cytomine bootstrap (see @cytomine-uliege & @cytomine).
TorecLuik/slurm-cluster
Docker local slurm cluster
TorecLuik/W_NucleiSegmentation-DeepCell
BIAFLOWS nuclei segmentation workflow using DeepCell 1.0.
TorecLuik/W_NucleiSegmentation-ImageJ
BIAFLOWS workflow to segment clustered nuclei using a laplacian filter, thresholding and a binary watershed transform.
TorecLuik/openmicroscopy
OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded by private and public research grants, OME has been a major force on the international microscopy stage since 2000.
TorecLuik/omero-py
Python project containing Ice remoting code for OMERO
TorecLuik/docker-from-omero-poc
proof-of-concept running docker container from omero web
TorecLuik/W_NucleiSegmentation-Stardist
Nuclei segmentation using Stardist
TorecLuik/rit-imageanalysis-containers
Making it easier for users to spin up a Singularity container with image analysis tools from a slurm-based cluster
TorecLuik/biaflows_jupyter_local
A jupyter-notebook that demonstrates the local use of BIAFLOWS, with SLURM
TorecLuik/omero-user-scripts-QBI
Plugins for OMERO from QBI-Microscopy