Component

A Component is an implementation of certain image processing / analysis algorithms.

Each component alone does not solve a Bioimage Analysis problem.

These problems can be addressed by combining such components into workflows.

Alignment of FIBSEM or SBFSEM images

Component
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Fiji CMTK GUI

Component
Description

Working version of a simple GUI frontend for CMTK image registration tools in Fiji

has topic
Imaging
Multimodal imaging
has function
Image registration
Affine registration
Deformable registration
need a thumbnail

Z-spacing correction for Fiji

Component
Description

Estimate the positions and spacing between sections (or at local points) of three dimensional image data. This method may be applied to any imaging modality that acquires 3-dimensional data as a stack of 2-dimensional sections. We provide plugins for both Fiji and TrakEM2.

has topic
Electron microscopy
has function
Warping
Image correction

Isotropic Super-Resolution for EM

Component
Description

Super-resolve anisotropic EM data along low-res axis with deep learning.

 

has topic
Electron microscopy
Focused ion beam scanning electron microscopy
Machine learning
has function
Image enhancement

McLuigi

Component
Description

Multicut workflow for large connectomics data. Using luigi for pipelining and caching processing steps. Most of the computations are done out-of-core using hdf5 as backend and implementations from nifty

has topic
Electron microscopy
has function
Image segmentation
Object classification
Classification
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