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.
|05/25/2018 - 17:30|
|Python||Software||05/25/2018 - 03:04|
|ImageScience.jar||Software||05/24/2018 - 03:29|
|06/06/2018 - 15:17|
|Tracking2.0||Software||05/24/2018 - 03:29|
|jMathPlot||Software||05/21/2018 - 01:22|
|Quality metric of 3D SPIM stacks||Software||Component||
An ImageJ/Fiji macro which measures quality through two stacks of images assumed to be acquired from two opposite angle of views using gray-level standard deviation.
|05/20/2018 - 21:03|
BM3D is a recent denoising method based on the fact that an image has a locally sparse representation in transform domain. This sparsity is enhanced by grouping similar 2D image patches into 3D groups. In this paper we propose an open-source implementation of the method. We discuss the choice of all parameter methods and confirm their actual optimality. The description of the method is rewritten with a a more transparent notation that in the original paper. A final index gives nonetheless the correspondence between the new notation and the original notation.
|05/20/2018 - 20:52|
It simulates a three-dimensional ground-truth that resembles aspects of a biological object like a spheroid. For each simulated view the signal is attenuated, convolved with an effective PSF, and anisotropically sampled using a Poisson process.
|05/20/2018 - 20:09|
|3D confocal noise simulator||Software||Component||
This Matlab code simulates the noise of the confocal laser scanning microscope depending on the depth in the image stack (serial sections). Using the stack of binary images, it applies different levels of noise in the signal and background parts of the images to simulate confocal images. This is useful for generating "virtual ground truth" images with known values of sample rotation and distortion.
|05/20/2018 - 19:59|
Mean shift is a filter which acts as edge preserving filter similarly to non local mean or anisotropic diffusion.
Mean shift can be used for denoising, segmentation or clustering. Two parameters are to be tuned, a spatial size of a patch and a gray level or color distance on which the algorithm is applied.
|05/20/2018 - 18:28|
|PHANTAST for FIJI||Software||Component||
|05/19/2018 - 11:33|
|05/18/2018 - 12:26|
|MATLAB Curve Fitting Toolbox||Software||05/16/2018 - 19:02|
|LOCI Bioformats plugin||Software||05/15/2018 - 00:32|
|Align slices in stack||Software||Component||
Align_slices in stack utilized the template matching function cvMatch_Template to do slice registration(alignment) based on a selected landmark.
Source code: link
|05/09/2018 - 04:04|
|Bioconductor||Software||05/08/2018 - 15:24|
|cvMatch_Template||Software||Component||05/09/2018 - 04:06|
|Template Matching and Slice Alignment--- ImageJ Plugins||Software||Collection||05/09/2018 - 04:08|
|Excel||Software||05/07/2018 - 18:29|