Load data

►An example set of data is provided and loads when the app is started. Different settings can be explored with these data
►Load your own data and the file type will be detected (csv, txt, xlsx are accepted and an Excel sheet number can be specified)
►Data should be supplied as one column of time and any number of columns of absorbances as shown in the example data provided
►Data files should not contain any gaps or spaces between characters and avoid unusual characters
►The default setting for clotting is 50% but can be adjusted
►The threshold value determines a lower value below which interpolation does not take place and can be increased if the analysis fails
►Noisy data or empty cells can cause the program to crash but more robust (though less accurate) curve analysis can be achieved by using a high threshold absorbance (e.g. 1)
►Accuracy may be improved, if interpolation is not used, by spline fitting and adding extra points (see below)

Baseline options

►These selections adjust the baseline for the start of clotting
►'Global zero' sets a baseline absorbance for all the curves to the same selected value
►'nth point' subtracts the absorbance value from a selected nth point from each curve (e.g first point or a point after lysis)
►'Min abs' finds and subtracts the lowest absorbance for each curve. An offset value can be added

Maximum options

►You can specify a global maximum or use the maximum clotting absorbance for each curve
►Global maximum may be useful if not all curves clot fully but you know what the final absorbance should be
►Global maximum is useful for Halo assays where some wells are used to provide a maximum absorbance for complete lysis using blood that is not clotted

Raw data or spline fitted data

►If data points are very sparse or you are using a high 'Threshold' value, it may be helpful to generate extra points using the spline fitting option
►Options for curve start, number of additional points and data trunction are provided for spline curve generation
►If you have good data with reasonable density of points simply use the defaults of raw data and interpolation
►Input data (raw or with extra fitted points, as selected), are shown in the plots in the Curve tab and data in the Raw Data tab

Graph options

►Displayed graphs and results table are presented in an adjustable arrangement
►Input the number of rows to display the plots and results as required (e.g. 8 rows for a full 96 well plate)
►Individual curves can be scrutinised on the next tab (Curve)
►These options do not affect data or calculated results

Select a parameter

►Select what should be shown in the results table
►The results table is organised like the graphical output above
►Values can be copied and pasted for further analysis

Other tabs

►'Curve' focuses on an individual well
►'All Results' is a table showing all results for each curve
►'Raw Data' is the time and absorbance data set. Time interval changes if spline fitted curves are used
►'Explore' presents graphical outputs of analysed results
►'Settings' generates a table of critical setings that can be recorded to help reproducibility
►Code files and detailed help notes are available in a github repository Here

Halo assays

►Settings on the app allow it to be used for halo assay data analysis [Bonnard et al, Sci Rep 7, 2346, 2017]
►Typically in this assay wells are included that give estimates for baseline and global maximum, which can be input into the app
►The high absorbance in the global max wells may mean the threshold needs to be increased and/or spline fitted data used
►The resulting lysis curves resemble clotting curves and results can be reported as time to 50% lysis (equivalent to 50% clotting in the app)

Changes in version 0.3

►Several changes have been made to the underlying code and appearance of Clot or Halo
►The code dealing with curve analysis should be more robust and efficient
►A new function is provided for reading user data which identifies the correct format of csv, txt, xlsx
►The default settings are to use interpolation of curves, but the option to avoid interpolation is set by increasing the 'Threshold' value
►Times at maximum rate increase are provided and shown on the clotting traces as a magenta line
►These results are calculated from smoothed first derivative curves

Please contact me with issues relating to:

Clot or Halo version 0.3.4, last accessed 2025-10-12

drclongstaff@gmail.com Links to other apps