Video Tutorials for BiofilmQ

We provide several tutorials to guide you step-by-step through BiofilmQ!

• 1. Introduction to BiofilmQ

• 1.1 How to download and install BiofilmQ

• 1.2 General overview over the BiofilmQ layout

• 1.3 File input

• 2.1 Image preparation

• 2.2 Segmentation

• 2.3 Parameter calculation

• 2.4 Time series analysis

• 2.5 Data export

• 3. Visualization

• 3.1 Basic plotting

• 3.2 Visualization Filtering

• 3.3 Advanced Visualization Options

1. Getting started

1. Introduction to BiofilmQ

Introduction to the concept of BiofilmQ

1.1 How to download and install BiofilmQ

1.2 General overview over the BiofilmQ layout

1.3 File input

1.3.1 Import of microscopy files

1.3.2 Import of custom tif files

2. Image processing

Overview over the different processing steps

2.1 Image preparation

Overview of the image preparation options

2.1.1 Separate micro-colonies for further processing

2.1.2 Register a time series prior to segmentation

2.2 Segmentation

Overview of the different steps of segmentation

2.2.1 Image cropping

2.2.2 Denoising

2.2.3 Thresholding

2.3 Parameter calculation

Extract object properties from segmented objects.

2.3.1 Fluorescence properties

2.4 Time series analysis

Cube lineage tracking

2.5 Data export

Export your results to Excel, .fcs and vtk files.

3. Visualization

3. Visualization Overview

Overview over the visualization tab

3.1 Basic plotting

3.1.1 Plotting options

3.1.2 Histogram plotting

3.1.3 2D XY-Plot per frameborder

3.1.4 Kymograph and Demograph plotting

3.1.5 Scatter plots

3.2 Visualization Filtering

Filtering objects prior to plotting

3.3 Advanced Visualization Options

Applying customs script on your data and plots

4. Workflows

4.1 Micro-colony analysis analogous to COMSTAT