Pinned Repositories
hrm
The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging for parallel batch deconvolutions.
hrm_docs
Huygens Remote Manager documentation
IceImarisConnector
IceImarisConnector is a simple commodity class that eases communication between Bitplane Imaris (http://www.bitplane.com) and MATLAB (http://www.mathworks.com) using the Imaris XT interface (http://www.bitplane.com/go/products/imarisxt).
obit
openBIS Importer Toolset (oBIT): this is a container project that references all server- and client-side components of oBIT as well as the installers.
pIceImarisConnector
pIceImarisConnector is a simple python class that eases communication between Bitplane Imaris (http://www.bitplane.com) and python (http://www.python.org) using the Imaris XT interface (http://www.bitplane.com/go/products/imarisxt).
pyND2SDK
Python wrapper for the Nikon ND2 SDK.
qu
Qu is an attempt to make the full deep learning workflow more interactive by providing a user interface (implemented as napari widget) that abstracts all steps from ground truth generation and curation to training and prediction.
qute
Leverages and extends several PyTorch-based framework and tools.
pyMINFLUX
Reader, analyzer, and viewer of MINFLUX raw data.
SpectraSorter
Software for droplet sorting based on the analysis of high-speed spectrophotometer (OceanFX) measurements.
aarpon's Repositories
aarpon/pyND2SDK
Python wrapper for the Nikon ND2 SDK.
aarpon/hrm
The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging for parallel batch deconvolutions.
aarpon/qu
Qu is an attempt to make the full deep learning workflow more interactive by providing a user interface (implemented as napari widget) that abstracts all steps from ground truth generation and curation to training and prediction.
aarpon/pIceImarisConnector
pIceImarisConnector is a simple python class that eases communication between Bitplane Imaris (http://www.bitplane.com) and python (http://www.python.org) using the Imaris XT interface (http://www.bitplane.com/go/products/imarisxt).
aarpon/hrm_docs
Huygens Remote Manager documentation
aarpon/obit_flow_core_technology
openBIS flow cytometry core technology.
aarpon/hrm_installer
Set of bash scripts for the automated installation and setup of the Huygens Remote Manager.
aarpon/obit_microscopy_core_technology
openBIS microscopy core technology.
aarpon/php-traditional-server_old
PHP-based server-side example for handling traditional endpoint requests from Fine Uploader
aarpon/qute
Leverages and extends several PyTorch-based framework and tools.
aarpon/pysspm
Simple Scientific Project Manager (sspm)
aarpon/aarpon.github.io
Personal page
aarpon/cellpose-napari
napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool
aarpon/centrosome
An open source image processing library
aarpon/FlowSOM
FlowSOM algorithm in Python, using self-organizing maps and minimum spanning tree for visualization and interpretation of cytometry data
aarpon/heteromotility
Quantitative analysis of cell motility behaviors
aarpon/hrm_ng
This is an attempt to rewrite the Huygens Remote Manager as a modern web application.
aarpon/imarisread
Imaris reader.
aarpon/napari-segment-blobs-and-things-with-membranes
A plugin based on scikit-image for segmenting nuclei and cells based on fluorescent microscopy images with high intensity in nuclei and/or membranes.
aarpon/nnUNet
aarpon/obit_annotation_tool
The Annotation Tool is part of the openBIS Importer Toolset (oBIT).
aarpon/obit_installer
The obit_installer downloads, configures and installs all client-side dependences of the openBIT Importer Toolset.
aarpon/obit_manager
obit_manager downloads, configures and installs all client-side dependences of the openBIT Importer Toolset. It also allows to update and reconfigure existing installations.
aarpon/obit_shared_core_technology
openBIS shared core technology: contains tools that are common to the flow and microscopy core technologies.
aarpon/pytorch-3dunet
3D U-Net model for volumetric semantic segmentation written in pytorch
aarpon/qute_api
API to manage deep-learning models and other artifacts.
aarpon/SDLMemory
Memory game written in C++ using the SDL library.
aarpon/SwissBIAS.github.io
Website for the SwissBIAS network: Swiss BioImage Analysts' network
aarpon/UNET-TGS
Applying UNET Model on TGS Salt Identification Challenge hosted on Kaggle
aarpon/useful_scripts
Collection of useful scripts.