Image Title Category Type Description Updated
need a thumbnail pystackreg Software Component

Python/C++ port of the ImageJ extension TurboReg/StackReg written by Philippe Thevenaz/EPFL.

A python extension for the automatic alignment of a source image or a stack (movie) to a target image/reference frame.

07/10/2018 - 17:17
Detection of Molecules - DoM Software Collection

A collection of components for super resolution image data:

  • Detect Molecules
  • Reconstruct Image
  • Results table
  • Drift correction
  • Chromatic correction
06/29/2018 - 12:27 Training Material 06/28/2018 - 02:31
Aivia Software Collection, Workflow 06/28/2018 - 02:31
need a thumbnail JDK Software 06/06/2018 - 15:16
need a thumbnail Temporal Plugin Software 06/05/2018 - 03:27
need a thumbnail Temporal Medial Filter Software Component

This component can be used to find moving foreground features, which can be a powerful way to suppress false background detections in subsequent tracking steps.

06/05/2018 - 03:27
need a thumbnail Fourier Bandpass Filter Software Component

This is a plugin bundled with native ImageJ.

See IJ reference for more details > Link

06/05/2018 - 03:32
Chainer Software Collection

Chainer is a Python-based deep learning framework aiming at flexibility. It provides automatic differentiation APIs based on the define-by-run approach (a.k.a. dynamic computational graphs) as well as object-oriented high-level APIs to build and train neural networks. It also supports CUDA/cuDNN using CuPy for high performance training and inference. For more details of Chainer, see the documents and resources listed above and join the community in Forum, Slack, and Twitter.

06/04/2018 - 17:46
need a thumbnail Python 2.7 Software 06/04/2018 - 15:13
QCAnet Software Component

Quantitative Criterion Acquisition Network (QCA Net) performs instance segmentation of 3D fluorescence microscopic images. QCA Net consists of Nuclear Segmentation Network (NSN) that learned nuclear segmentation task and Nuclear Detection Network (NDN) that learned nuclear identification task. QCA Net performs instance segmentation of the time-series 3D fluorescence microscopic images at each time point, and the quantitative criteria for mouse development are extracted from the acquired time-series segmentation image.

06/04/2018 - 15:13
need a thumbnail Libtiff Software 05/31/2018 - 21:58
need a thumbnail ImageMagick Software 05/31/2018 - 21:58
need a thumbnail GNU Parallel Software 05/31/2018 - 21:58
need a thumbnail bftools Software 05/31/2018 - 21:58
need a thumbnail MATLAB Signal Processing Toolbox Software 05/30/2018 - 00:36
need a thumbnail matplotlib Software 05/27/2018 - 19:47
Manual tracking with TrackMate Software Component

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

05/27/2018 - 17:36
GIMP Software Collection

This is the official website of the GNU Image Manipulation Program (GIMP).

GIMP is a cross-platform image editor available for GNU/Linux, OS X, Windows and more operating systems. It is free software, you can change its source code and distribute your changes.

Whether you are a graphic designer, photographer, illustrator, or scientist, GIMP provides you with sophisticated tools to get your job done. You can further enhance your productivity with GIMP thanks to many customization options and 3rd party plugins.

05/27/2018 - 16:31
Log3D Software Component

The freely available software module below is a 3D LoG filter. It applies a LoG (Laplacian of Gaussian or Mexican Hat) filter to a 2D image or to 3D volume. Here, we have a fast implementation. It is a perfect tool to enhance spots, like spherical particles, in noisy images. This module is easy to tune, only by selecting the standard deviations in X, Y and Z directions.

IJ Macro command example

run("LoG 3D", "sigmax=1 sigmay=1 sigmaz=13 displaykernel=0 volume=1");
05/25/2018 - 19:07