Image enhancement moves further away from the reality, as opposed to Image reconstruction that moves closer to the reality.

Synonyms
Image restoration

Paintera

Description

Paintera is a general visualization tool for 3D volumetric data and proof-reading in segmentation/reconstruction with a primary focus on neuron reconstruction from electron micrographs in connectomics. It features/supports:

  •  Views of orthogonal 2D cross-sections of the data at arbitrary angles and zoom levels
  •  Mipmaps for efficient display of arbitrarily large data at arbitrary scale levels
  •  Label data
    •  Painting
    •  Manual agglomeration
    •  3D visualization as polygon meshes
      •  Meshes for each mipmap level
      •  Mesh generation on-the-fly via marching cubes to incorporate painted labels and agglomerations in 3D visualization. Marching Cubes is parallelized over small blocks. Only relevant blocks are considered (huge speed-up for sparse label data).

Paintera is implemented in Java and makes extensive use of the UI framework JavaFX

Paintera screenshot

CSBDeep, a toolbox for Content-aware Image Restoration (CARE) in Fiji

Description

Deep learning for fluorescence image restoration (denoising, deconvolution). Requires training on your data set but the procedure is described.

CARE

Scipion

Description

Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows you to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.

http://scipion.cnb.csic.es/m/home/

SIMToolbox

Description

SIMToolbox: a MATLAB toolbox for structured illumination microscopy SIMToolbox is an open-source, modular set of functions for MATLAB designed for processing data acquired by structured illumination microscopy. Both optical sectioning and super-resolution applications are supported. The software is also capable of maximum a posteriori probability image estimation (MAP-SIM), an alternative method for reconstruction of structured illumination images. MAP-SIM can potentially reduce reconstruction artifacts, which commonly occur due to refractive index mismatch within the sample and to imperfections in the illumination. 2665

SIMToolbox

fairSIM

Description

An easy-to-use plugin that provides SR-SIM reconstructions for a wide range of SR-SIM platforms directly within ImageJ. For research groups developing their own implementations of super-resolution structured illumination microscopy, fairSIM takes away the hurdle of generating yet another implementation of the reconstruction algorithm. For users of commercial microscopes, it offers an additional, in-depth analysis option for their data independent of specific operating systems. As a modular, open-source solution, fairSIM can easily be adapted, automated and extended as the field of SR-SIM progresses. 2662

 

has function
from FairSIM documentation