All functions

Spots.as.dataframe()

Convert MaMuT xml Spots tags to a dataframe 
Tracks.as.dataframe()

Convert MaMuT xml Tracks tags to a dataframe 
add_mic_loc()

Calculating coordinates in pixels 
add_px_loc()

Calculating coordinates in pixels 
checkTrack()

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. 
countSpot()

Counting spots per timepoints 
getFluo()

Extracting fluorescence values
Extracting fluorescence values in an .h5 file in the BigDataViewer format around given coordinates 
get_registration()

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. 
heatmap2int()

Conversion of continuous variable to discrete integers for visualisation in MaMuT 
hex2int()

Converting HEX colors to MaMut integer color scale 
int2hours()

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. 
makeSpotNode()

Create a spot node
To modify the mamut.xml file. 
mmFluo()

Calculate a mean and median fluorescent value for each spot/cell 
mmFluo_all()

Calculate mean and median fluorescent values for individual cells, per timepoin and for the whole movie 
mmFluo_perT()

Calculate a mean and median fluorescent value for all spots of each timepoints 
mmFluo_wholeMovie()

Calculate a mean and median fluorescent value for the whole movie over all spots 
modifyXML()

Modify MaMuT .xml file
Update values of existing parameters and/or add the manual color parameter 
posLoc2posWorld()

Calculating the coordinates
N.B.: pos_world = (3DHASHING) x (CALIBRATION) x pos_local 
prod_affine_registration()

Product of affine transformations 
read_ViewRegistration()

Get information relative to registration in .xml Big Data Viewer files 
spots.and.tracks()

Combining spots and tracks dataframes 
track2plot()

Plotting tracks
Plotting MaMuT tracks with custom color code 
vect2mat()

Takes a 12 coordinates vector and returns a 4x4 matrix 