Forrest Gump and spatial cross-correlation (part 1)

Last couple of weeks I was reading, coding and playing with spatial/temporal cross-correlation for microscopy image/movie analysis. I’m going to summarize my findings in a series of posts, before I forget everything. It is going to be a long story, so buckle up. First of all, motivation, or why would one use cross-correlation (before explanation…
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How does a kymograph sound like?

This post is mostly for fun and educational purposes. So, there are a lot of common methods in areas of sound and image processing. For example, Fourier, wavelet transforms are used heavily for analysis and compression of both audio and video. In addition there are a lot of different denoising filters based on the same…
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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…
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Microscopy acquisition limits for Single Particle Tracking (SPT)

It is not very clear, how biological systems (cells in particular) can bridge amazing ranges of scales in time and space.  To study these processes one would need a corresponding multi-scale measurement device (in theory). But microscope, for example, by default is one-scale instrument. Meaning that in 99% of movie acquisitions there is only one time scale….
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Multiscale Trend Analysis code

In many areas of science (sociology, intracellular transport, stock exchange, climatology, etc) there is a need to decompose observed noisy time series into a set of piecewise linear trends. Let me show a typical example data that I’ve generated myself: Alternative to linear trends analysis method is Fourier transform (for example). But it assumes that…
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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. Live: Twice per year Bioimaging Utrecht organizes “Image analysis using ImageJ/FIJI” workshop in Utrecht University. Next one will happen on 7th of April. Here is the poster with location and time details. The…
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Different views of cells

Some bits of my current work.  Relatively recent development of superresolution technique provided tools to see the shape and sub-structure of cells in much more details. Here is example: live image of HeLa cells labelled with membrane fluorescent marker (mEos) in regular widefield (top-left half) and in superresolution (SR) reconstruction: There is quite a difference,…
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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…
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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. Ideally software that makes kymograph…
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