Rendering colorcoded 3D localization microscopy results

In many scientific applications there is a need to build a 2D map of some value, kind of 2D distribution or strictly speaking 2D function. Most of the time the area is discrete, i.e. pixelated. Often it is done in one 2D picture using density plot, where the value of function at point x,y is represented by the brightness of the pixel with coordinates x and y. In superresolution localization microscopy resulting pictures are often rendered as 2D “probability density functions”. I.e. each pixel’s brightness reports a probability to observe some number of molecules at given volume, taken from some measurements (microscopy acquisition). But what should be done if one wants to show on the same picture two 2D functions simultaneously? For example, for localization microscopy, combine probability and also Z-coordinate?

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Curve extraction plugin

Brief intro:
About a year ago me and Jalmar were working on the automated methods of line/curve extraction from images (mostly microtubules in microscopy pictures, but not limited to). There are a lot of different methods, but after some research we concluded that one of the basic and “essential baseline control” was Carsten Steger’s “An Unbiased Detector of Curvilinear Structures” published in 1996 (~830 citations since then). The paper describes method in all details and what is even more interesting, there was a link to ftp with open source code. Unfortunately almost 20 years later this ftp was down and so we tried to reconstruct code according to description in the paper with some success. (continue reading…)

FIJI/ImageJ workshops: live and offline

If you are around the Netherlands, here is some information for the coming workshop. If not, scroll down to get link to the offline version.
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Particle tracking plugins file formats and converter

Recently I’ve  been working on projects involving heavy usage of particle tracking. There are many available solutions to do that, but since I’m a big fan of ImageJ/FIJI, I’m sticking to it. Among multiple plugins for tracking there are two best options (in my opinion): TrackMate for the automatic tracking and MTrackJ for the manual and track editing/visualization.
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Why another kymograph ImageJ plugin?

Kymograph is a useful tool to transform a movie containing particles movement into a single picture/figure. It is convenient when analyzing vesicles movement in cells, axons/dendrites of neurons, cars movement on roads. It shows particles’ speed, direction, intensity, etc.  What it does is just plotting how intensity is changing over time along some line or curve.  (continue reading…)