aarpon

pyND2SDK

Python wrapper for the Nikon ND2 SDK.

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.

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.

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).

hrm_docs

Huygens Remote Manager documentation

obit_flow_core_technology

openBIS flow cytometry core technology.

hrm_installer

Set of bash scripts for the automated installation and setup of the Huygens Remote Manager.

obit_microscopy_core_technology

openBIS microscopy core technology.

php-traditional-server_old

PHP-based server-side example for handling traditional endpoint requests from Fine Uploader

pysspm

Simple Scientific Project Manager (sspm)

qute

Leverages and extends several PyTorch-based framework and tools.

aarpon.github.io

Personal page

cellpose-napari

napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool

centrosome

An open source image processing library

FlowSOM

FlowSOM algorithm in Python, using self-organizing maps and minimum spanning tree for visualization and interpretation of cytometry data

heteromotility

Quantitative analysis of cell motility behaviors

hrm_ng

This is an attempt to rewrite the Huygens Remote Manager as a modern web application.

imarisread

Imaris reader.

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.

nnUNet

obit_annotation_tool

The Annotation Tool is part of the openBIS Importer Toolset (oBIT).

obit_installer

The obit_installer downloads, configures and installs all client-side dependences of the openBIT Importer Toolset.

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.

obit_shared_core_technology

openBIS shared core technology: contains tools that are common to the flow and microscopy core technologies.

pytorch-3dunet

3D U-Net model for volumetric semantic segmentation written in pytorch

qute_api

API to manage deep-learning models and other artifacts.

SDLMemory

Memory game written in C++ using the SDL library.

SwissBIAS.github.io

Website for the SwissBIAS network: Swiss BioImage Analysts' network

UNET-TGS

Applying UNET Model on TGS Salt Identification Challenge hosted on Kaggle

useful_scripts

Collection of useful scripts.