Using Cellprofiler to count viral particles (II)



Input Modules – Images

This is the second post in a series that will eventually describe the entire process of counting viral particles. Before we can start analysing images, we have to get the image data into Cellprofiler. The program uses a series of input modules to do this. After correctly configuring the “Input modules” section of Cellprofiler it will know:

  1. where to find the images you need to analyze
  2. whether or not to extract/import metadata
  3. how to assign names to the images for subsequent internal reference during the processing
  4. whether to assign each image to a group.

In my case, when the “Images” input module was selected, I was able to drag/drop the image into the “File List” area (See the image to the left- “Input Modules – Images”). Now Cellprofiler knows where my image is. After I’ve developed this pipeline completely, I can drag a files or folders full of files here for batch analysis.

I didn’t want Cellprofiler to extract metadata, so I selected the “No” radio button next to the  “Extract metadata?” question in the Metadata input module (See the image “Input Modules – Metadata”).


Input Modules-Metadata

This module allows you to extract and store information about your image (e.g. pixel size, well/plate information, channel wavelengths, etc) along with your analysis. Options in this module allow Cellprofiler to extract metadata from the image header, the image name, or a separate file containing the metadata.


Input Modules – Names and Types

The NamesAndTypes module allows you to assign meaningful names to images and informs Cellprofiler whether the input image is colour, grayscale, or binary. In my example, I’ve called the input image “StartingImage”. Each module that outputs an image will require you to name the output image for downstream processing. Often, the output image from one module becomes the input image for the next module in the pipeline, therefore you should name your images something short but intuitive that describes what has just happened to it. The final setting for this module asks about where Cellprofiler should get the bit-depth information

The last module in the Input Modules section is called “Groups”. This module lets you categorise your images into groups based on plates, wells, positions, size, frame, etc. It’s designed for flexibility to let you process groups independently. I don’t want to categorise my imges so I left the “No” radio button ticked. This concludes how Cellprofiler gets image data into its analysis section, see the next post for details of the initial processing and illumination correction modules.