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

Detection of Molecules - DoM

Description

A collection of components for super resolution image data:

  • Detect Molecules
  • Reconstruct Image
  • Results table
  • Drift correction
  • Chromatic correction

Manual tracking with TrackMate

Description

Manual tracking using Trackmate plugin (comes with FIji, so no installation required if you are using Fiji). 

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ImagePy

Description

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis.

CompuCell3D

Description

CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in-silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. CompuCell3D models have been used to solve basic biological problems, to develop medical therapies, to assess modes of action of toxicants and to design engineered tissues. CompuCell3D intuitive and make Virtual Tissue modeling accessible to users without extensive software development or programming experience.

It uses Cellular Potts Model to model cell behavior.

Docker ParaViewWeb

Description

This ParaViewWeb Docker container is used by the Galaxy Project.  Paraview is an VTK based visualization server, for 3D.

ParaViewWeb in Galaxy

Orbit

Description

Orbit Image Analysis is a free open source software with the focus to quantify big images like whole slide scans.

It can connect to image servers, e.g. Omero.
Analysis can be done on your local computer or via scaleout functionality in a distrubuted computing environment like a Spark cluster.

Sophisticated image analysis algorithms incl. tissue quantification using machine learning, object segmentation and classification are build in. In addition a versatile API allows you to enhance Orbit and to run your own scripts.

Orbit

MaMuT

Description

MaMuT is an end user plugin that combines the BigDataViewer and TrackMate to provide an application that allow browsing, annotating and curating annotations for large image data.

Gaussian blur in ImageJ

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Create new TrakEM project in Fiji

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