All functions
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Spots.as.dataframe()
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Convert MaMuT xml Spots tags to a dataframe |
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Tracks.as.dataframe()
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Convert MaMuT xml Tracks tags to a dataframe |
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add_mic_loc()
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Calculating coordinates in pixels |
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add_px_loc()
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Calculating coordinates in pixels |
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checkTrack()
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Check order of Track_df
Function checks if spots source and spots target in Track_df are inverted compared to frame and invert if necessary so that source always corresponds to the smaller frame and target to the biggest one. |
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countSpot()
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Counting spots per timepoints |
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getFluo()
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Extracting fluorescence values
Extracting fluorescence values in an .h5 file in the BigDataViewer format around given coordinates |
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get_registration()
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Get information relative to registration in ViewTransform node of Big Data Viewer files
Registration based on affine transforms, one or several, written as a vector of 12 indices
This vector can be transformed as a 4x4 matrix by adding 0,0,0,1 at the end of the vector and reading it by row. |
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heatmap2int()
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Conversion of continuous variable to discrete integers for visualisation in MaMuT |
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hex2int()
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Converting HEX colors to MaMut integer color scale |
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int2hours()
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Convert an integer to hour minutes in digital format
Assumes that integers (0, 1, 2) refers to 30 minutes timesteps (00:00, 00:30, 01:00)... Same function as in cellviz3d. |
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makeSpotNode()
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Create a spot node
To modify the mamut.xml file. |
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mmFluo()
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Calculate a mean and median fluorescent value for each spot/cell |
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mmFluo_all()
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Calculate mean and median fluorescent values for individual cells, per timepoin and for the whole movie |
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mmFluo_perT()
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Calculate a mean and median fluorescent value for all spots of each timepoints |
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mmFluo_wholeMovie()
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Calculate a mean and median fluorescent value for the whole movie over all spots |
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modifyXML()
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Modify MaMuT .xml file
Update values of existing parameters and/or add the manual color parameter |
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posLoc2posWorld()
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Calculating the coordinates
N.B.: pos_world = (3D-HASHING) x (CALIBRATION) x pos_local |
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prod_affine_registration()
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Product of affine transformations |
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read_ViewRegistration()
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Get information relative to registration in .xml Big Data Viewer files |
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spots.and.tracks()
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Combining spots and tracks dataframes |
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track2plot()
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Plotting tracks
Plotting MaMuT tracks with custom color code |
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vect2mat()
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Takes a 12 coordinates vector and returns a 4x4 matrix |