Component

HyphaTracker propose a workflow for time-resolved analysis of conidia germination. Each part of this workflow can also be used independnatly , as a toolbox. It has been tested on bright-field microscopic images of conidial germination. Its purpose is mainly to identify the germlings and to remove crossing hyphae, and measure the dynamics of their growth.

LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation

Download instruction:

There is no download but you can easily install this plugin via ImageJ update site. If you reallu need to download the jar file, access the file in the update site repository (Link)

Kymograph generation under ImageJ:

one simple solution, plot a line (ROI line) on the first frame, where you want to generate the kymograph.

Use

Image  / Stacks  / Reslice

It will generate a new image were Y dimension is the time, and X the position on the line you have drawn.

This filter uses convolution with a Gaussian function for smoothing. Sigma is the radius of decay to exp(-0.5) ~ 61%, i.e. the standard deviation sigma of the Gaussian (this is the same as in Photoshop, but different from earlier versions of ImageJ, where a value 2.5 times as much had to be entered.

Like all ImageJ convolution operations, it assumes that out-of-image pixels have a value equal to the nearest edge pixel. This gives higher weight to edge pixels than pixels inside the image, and higher weight to corner pixels than non-corner pixels at the edge. Thus, when smoothing with very high blur radius, the output will be dominated by the edge pixels and especially the corner pixels (in the extreme case, with a blur radius of e.g. 1e20, the image will be raplaced by the average of the four corner pixels).

For increased speed, except for small blur radii, the lines (rows or columns of the image) are downscaled before convolution and upscaled to their original length thereafter.

Drishti (from Sanskrit  word for "vision" or "insight") is a multi-platform, open-source volume-exploration and presentation tool. Written for visualizing tomography data, electron-microscopy data and the like.