Data sharing

Neuroglancer

Description

Web based viewer developped for google for very big data: 

Neuroglancer is a WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons). The segmentation has to be done before loading the dataset, it is not done Inside the viewer.

This is not an official Google product.

It has among other the nice feature of beeing able to generate url for sharing a specific view.

Note that the only supported browser for now are 

  • Chrome >= 51
  • Firefox >= 46

 

Neuroglancer

Ikosa

Description

online image data management system which supports authenticated image upload, cloud-based storage, project-based management and viewing of standard and whole slide images. One can use different annotation tools to highlight important objects or areas within images. It is the first basic version and new features such as sharing for easy collaboration with your colleagues or first automated analysis applications based on artificial intelligence will be added soon.

Ikosa Portal: multi user image data management

Ikosa Prisma: Automated Image Analysis based on deep learning (available in summer 2019)

Free if limited to 2 users and 1 gigabyte, otherwise montly fees.

 

ikosa

BisQue

Description

Bisque (Bio-Image Semantic Query User Environment) : Store, visualize, organize and analyze images in the cloud. It also allow to run workflows using a set of deployed tools, such as CellProfiler, RootTipMultin Nuclear Tracker, Microtubule tracker etc...

Bisque was developed for the exchange and exploration of biological images.

The Bisque system supports several areas useful for imaging researchers from image capture to image analsysis and querying. The bisque system is centered around a database of images and metadata. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content.

  • Bisque is free and open-source
  • Flexible textual and graphical annotations
  • Cloud scalability: PBs of images, millions of annotations
  • Distributed storage: local, iRODS, S3
  • Integrated image analysis, high-throughput with Condor
  • Analysis in MATLAB, Python, Java+ImageJ
  • 100+ biological image formats
  • Very large 5D images (100+ GB)
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Openimadis

Description

OpenImadis stands for Open Image Discovery: A platform for Image Life Cycle Management. It was previously called CID iManage (for Curie Image Database).

No image data conversions, no duplication.

- Uploads data to a secure server in the original format

- Unique id for data

Supports sharing and collaboration with access control

- Allows users to upload, view, update or download data based on their access privileges

Supports multiple ways of attaching meta-information

- Annotations, comments and file attachments

-Analysis results as query-able visual objects

Supports Archiving (data moving to another long-term storage but still searchable)

Facilitates custom visualization and analysis

- Access data from preferred analysis and visualization tools

- Access relevant bits of data to build efficient web and mobile application

Facilitate easy access to analysis and visualization applications hosted on other servers

- Run analysis on dedicated compute clusters

- Access applications hosted and published by other users

Highly Scalable

- Supports on-the-fly addition of server nodes to scale concurrent usage

 

 

openImadis

ScientiFig

Description

ScientiFig is a free tool to help you create, format or reformat scientific figures. It comes either as a stand alonesoftware, either as a Fiji/IJ plugin.

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scientifig

Shiny - R package

Description

Shiny is an R package that makes it easy to build interactive web apps straight from R.

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FigureJ

Description

This plugin achieves easy creation of image figures for publications, reports, projects.

  • Easy-to-design interactive figure layout.

  • Visually assign image content to panels.

  • High-quality image scaling and rotation.

  • Easy and consistent panel labels and scale bars.

  • Each panel has it's original datasource's properties and tracks achieved image processing.

  • Save and re-open editable figures.

  • Export as standard image formats with textual description of each panel history.

Compared to Make montage, the plugin adds more flexibility to montage creation: Easy-to-design interactive figure layout. Visually assign image content to panels. High-quality image scaling and rotation. Easy and consistent panel labels and scale bars. Each panel has it's original data source's properties and tracks achieved image processing. Save and re-open editable figures. Export as standard image formats with textual description of each panel history. 

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FigureJ

Cytomine

Description

Cytomine is a rich internet application using modern web and distributed technologies (Grails, HTML/CSS/Javascript, Docker), databases (spatial SQL and NoSQL), and machine learning (tree-based approaches with random subwindows) to foster active and distributed collaboration and ease large-scale image exploitation.

It provides remote and collaborative principles, rely on data models that allow to easily organize and semantically annotate imaging datasets in a standardized way (using user-defined ontologies associated to regions of interest), efficiently support high-resolution multi-gigapixel images (incl. major digital scanner image formats), and provide mechanisms to readily proofread and share image quantifications produced by any image recognition algorithms.

By emphasizing collaborative principles, the aim of Cytomine is to accelerate scientific progress and to significantly promote image data accessibility and reusability. Cytomine allows to break common practices in this domain where imaging datasets, quantification results, and associated knowledge are still often stored and analyzed within the restricted circle of a specific laboratory.

This software is e.g. being used by life scientists in to help them better evaluate drug treatments or understand biological processes directly from whole-slide tissue images (digital histology), by pathologists to share and ease their diagnosis, and by teachers and students for pathology training purposes. It is also used in various microscopy applications.

Cytomine can be used as a stand-alone application (e.g. on a laptop) or on larger servers for collaborative works.

Cytomine implements object classification, image segmentation, content-based image retrieval, object counting, and interest point detection algorithms using machine learning.

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Magic Montage

Description

This tool adds to ImageJ functions to build and organize montages. It comes with the ImageJ installer but can also be downloaded from the ImageJ wiki. A video tutorial is available.

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CATMAID

Description

**Collaborative Annotation Toolkit for Massive Amounts of Image Data** CATMAID is a Collaborative Annotation Toolkit for Massive Amounts of Image Data. It is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by GoogleMaps, with which it shares basic navigation concepts, enhanced to allow the exploration of 3D biological image data acquired by optical or physical sectioning microscopy techniques. The interface enables seamless sharing of regions of interest through bookmarks and synchronized navigation through multiple registered data sets. With massive biological image data sets it is unrealistic to create a sustainable centralized repository. A unique feature of CATMAID is its partially decentralized architecture where the presented image data can reside on any Internet accessible server and yet can be easily cross-referenced in the central database. In this way no image data are duplicated and the data producers retain full control over their images. CATMAID is intended to serve as data sharing platform for biologists using high-resolution imaging techniques to probe large specimens. Any high-throughput, high-content imaging project such as gene expression pattern screens would benefit from the interface for data sharing and annotation.

CATMAID