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Custom Analysis Part 1

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Renske van Raaphorst edited this page Oct 31, 2019 · 2 revisions

Before you get started

  1. Start R & load BactMAP. Find installation & loading instructions for BactMAP here.
  2. Get the datasets needed for the tutorial through this link. This is the same data collection as used in the previous tutorial, Plotting Temporal Localization. If you haven't already, download the zip file and extract & save it on your computer. If you want to do this tutorial using your own data, check BactMAP’s import functions here.
  3. Set the working directory of your R session to the extracted folder "Time-Lapse-Analysis". Specify the path using the command setwd(), for example:
setwd("C:/the/path/to/Time-Lapse-Analysis")
⬅️ Custom Analysis: Overview ▪️ ◾ ▪️ Custom Analysis Part 2: Data Import ➡️

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
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