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cellpose-napari

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

centrosome

An open source image processing library

fine-uploader

Multiple file upload plugin with image previews, drag and drop, progress bars. S3 and Azure support, image scaling, form support, chunking, resume, pause, and tons of other features.

flowsom

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

fourierconvolutioncudalib

Implementation of 3d non-separable convolution using CUDA & FFT Convolution

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

hrm_installer

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

hrm_ng

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

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).

imarisread

Imaris reader.

imarisselector

ImarisSelector allows picking the module licenses to check out when Imaris starts and allows an administrator to configure Imaris for all users.

matlab-tree

A MATLAB class to represent the tree data structure.

matlabstarter

A series of startup functions for MATLAB that dynamically adds MATLAB m files, Java folders and .jar archives in user-defined folders and optionally updates any subversion or git working copies found.

ml_21092017

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

openBIS Importer Toolset (oBIT): this is a container project that references all server- and client-side components of oBIT as well as the installers.

obit_annotation_tool

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

obit_datamover_jsl

The Datamover_JSL module is part of the openBIS Importer Toolset (oBIT).

obit_flow_core_technology

openBIS flow cytometry core technology.

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_microscopy_core_technology

openBIS microscopy core technology.

obit_shared_core_technology

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

php-traditional-server

A set of classes to support file uploading from FineUploader. Born from the ashes of the original project.

php-traditional-server_old

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

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.