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Segmentation Tutorial Part 1

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vrrenske edited this page Oct 24, 2019 · 4 revisions

Before getting Started

  1. Start R & load BactMAP. Find installation & loading instructions for BactMAP here.
  2. Get the tutorial files on your computer. Download the tutorial datasets here. Unzip and save the files on your computer.

Check the documentation of the Staphylococcus aureus subset here and the Streptococcus pneumoniae subset here.

  1. Now set your working directory to the folder where you saved the tutorial files.

There are multiple ways to set your working directory: using the terminal, by prompting a GUI, or within Rstudio:

setwd("type_the_correct_path_here")
#or
setwd(choose.dir()) #directory picker GUI, doesn't work in MAC!
#or

Setting the working directory in Rstudio

⬅️ Comparing Segmentation: Overview Segmentation Tutorial 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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