General Workflow

In general, a typical BactMAP workflow follows three steps:

Data Import - Combining Data - Plotting

Optionally, this will be followed by a last step, custom analysis.

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Data Import

You can find information on all the import methods here.

Combining Data

If you import data from multiple programs or want to connect multiple fluorescent channels or experimental conditions, you need to connect the data to each other. You can find the methods for connecting data sets under Data Import & Conversion:

1. Adding spot or object information to segmentation data.
2. Combine conditions and/or channels
3. Add TIFF information to segmentations

Plotting

To get to know the plotting options within BactMAP, check out the plotting overview.

Custom Analysis

BactMAP aims to put your data in such a format, that it is possible to do your own custom analysis in R from here (or in another program of choice). Check out the tutorial on custom analysis and read through the Utilities (see the Side Bar on the right). If you want to continue in another program, find here how to save your data.

Example Workflows

If you are running the same analysis multiple times, it can be helpful to automate the process. Download the example scripts below of typical workflows:

1. Import from Oufti: Plot Overview with createPlotlist ➡️ Save all plots
2. Import Morphometrics files from different conditions ➡️ Combine the files ➡️ Plot Distributions
3. Import timelapse from SuperSegger ➡️ Plot all Seperate Kymographs ➡️ Save Data

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Do you have a workflow in a typical order? Don't hesitate to send me an email for help building your own standardized script.