Fluorescence microscopy

The purpose of the workflow is ....

First you need

  FlyLimbTracker is  a method that uses active contours to semi-automatically track body and leg segments from video image sequences of unmarked, freely behaving Drosophila flies. This approach can be used to measure leg segment motions during a variety of locomotor and grooming behaviors.

For now the plugin have to be downlaoded directly from the EPFL website (see link), not from the search bar as usual in ICY.

Classification of trajectoire: need tracking results as input and will then classify the trajectories as  brownian motion, confined brownian or directed.

SliceMap

Whole brain tissue slices are commonly used in neurobiological research for analyzing pathological features in an anatomically defined manner. However, since many pathologies are expressed in specific regions of the brain, it is necessary to have an annotation of the regions in the brain slices. Such an annotation can be done by manual delineation, as done most often, or by an automated region annotation tool.

SliceMap is a FIJI/ImageJ plugin for automated brain region annotation of fluorescent brain slices. The plugin uses a reference library of pre-annotated brain slices (the brain region templates) to annotate brain regions of unknown samples. To perform the region annotation, SliceMap registers the reference slices to the sample slice (using elastic registration plugin BUnwarpJ) and uses the resulting image transformations to morph the template regions towards the anatomical brain regions of the sample. The resulting brain regions are saved as FIJI/ImageJ ROI’s (Regions Of Interest) as a single zip-file for each sample slice.

More information can also be found in "SliceMap: an algorithm for automated brain region annotation", Michaël Barbier, Astrid Bottelbergs, Rony Nuydens, Andreas Ebneth, Winnok H De Vos, Bioinformatics, btx658, https://doi.org/10.1093/bioinformatics/btx658

Software for analysis, visualization, simulation, and acquisition  of data from spectroscopy and fluorescence microscopy.

• Fluorescence Correlation Spectroscopy (FCS)
• Fluorescence Lifetime Imaging (FLIM) and Phasor plots
• Förster Resonance Energy Transfer (FRET)
• Generalized Polarization (GP) and Spectral Phasors
• Number and Brightness (N&B)
• Photon Counting Histogram (PCH)
• Raster and Spatio-temporal Image Correlation Spectroscopy (RICS and STICS)
• Single Particle and Modulation Tracking (SPT, MT)
• Image Mean Square Displacement (iMSD)
• Pair correlation function (pCF)