Skip to content

Tutorials

Jump to bottom
Renske van Raaphorst edited this page Mar 23, 2022 · 11 revisions

The tutorials below recreate the figures from our publication on bactMAP:

  1. Plotting Localization
  2. Comparing Segmentation Results
  3. Time-Lapse Analysis part 1: Plotting Temporal Localization
  4. Time-Lapse Analysis part 2: Custom Analysis (advanced)

Extra tutorials:

  1. Genealogy

Note that you can also find example code in the documentation (plotting & utilities).

Getting Started

  1. Download & Install
  2. Tutorials
  3. General Workflow

Data Import & Conversion

  1. Import Data
  2. Add Localization to Segmentation
  3. Combine Conditions & Channels
  4. Saving Data

Plotting

  1. Overview
  2. Using TIFFs
  3. Localization
  4. Timelapse

Utilities

  1. Color Palettes
  2. Pixel-Micron Conversion
  3. Working with Large Data Sets
  4. Version Compatibility

Data Structure

  1. Mesh
  2. Spots
  3. Objects
  4. Raw Images
  5. Phylogeny
  6. cellList

Example Datasets

  1. Example Dataframes
  2. Origin Localization
  3. Time-Lapse of DnaX and FtsZ
  4. Comparing Segmentations 1
  5. Comparing Segmentations 2

Contact us

  1. Report an issue
  2. email
Clone this wiki locally