3. Working with Projects and Markersets

The project-based concept used in the cellXpress provides a flexible and systematic way to organize image analysis tasks across multiple plates and different sets of fluorescence markers. A single project can contain multiple plates as well as different sets of markers. This gives users the flexiblity to perform analyses with different combinations of the available markers, using the same set of source images.

The basic procedure for creating a new cellXpress project is:

3.1. Set cellXpress Root directory paths

The cellXpress uses three "root" directories to track and manage data: the Project, Data and Raw Data root directories. This allows cellXpress to link together and synchronize the different types of raw and intermediate data associated with each project. Use of a central repository for the root directories facilitates cross-platform collaboration and permits multiple users to access and analyze the same physical datasets, even if they are using different machines or operating systems. Thus, the need to create and manage multiple copies of the image data is avoided.

Configuration files, extracted features and analysis results are stored under the Project root directory, while the corresponding images used for the analyses are stored under the Data and Raw Data root directories. Root directory paths can be set as follows:

  • [cellXplorer]: Option>Root path
  • Project root directory: "D:\Projects"
  • Data root directory: "D:\Projects"
  • Raw Data root directory: "D:\Microscope"
  • Click "OK" to accept
images/Ch3_project-root-dir.png

3.2. Create a new project

Once the root directories are set, create a directory for the new project under the Project root path. Next, via the Project menu in cellXpress, create a new Project by specifying the project name, project directory path and plate type (96-well or 384-well):

  • [cellXplorer]: Project>Create new project
  • [New project]: Project name: "Drosophila_kc167""
  • [New project]: Project path: "D:\Projects\121122_FirstProject\projects\121119-Drosophila_kc167"
  • [New project]: Select plate type: 96
  • [New project]: Use "Add single…" or "Add multiple…" to find and add plate data.
  • [New project]: Plate list: "D:\Projects\121122_FirstProject\plates\000-121119-kc167-Example_data-DL10001"
  • [New project]: Click "OK" to accept
images/Ch3_new-project.png

3.3. Create markersets

After the new Project is created, define one or more markersets, according to the markers or image channels to be used for analysis. Markerset parameters, including channel names, index numbers can be set here, along with various display parameters.

  • [cellXplorer]: Markerset>Add new markerset
  • [New markerset]: Markerset name: DNA/CH2/CH3
  • [New markerset]: Marker number: 3
  • [New markerset]: Segmentation method: Multimarker watershed
  • [New markerset]: Define Markerset parameters
  • [New markerset]: Click "OK" to accept
images/Ch3_set-markerset.png

3.4. Add wells using the Well List manager

Each project uses one or more Well Lists to manage the collection of wells on the plates to be analyzed. Use the Well List panel in the cellXplorer window to select, add or remove wells from a project. Single wells or groups of wells can be associated with a markerset for specific analysis tasks.

The Well List manager:

  • Auto select wells: Select all non-empty wells
  • New: Create the new well list
  • Remove: Remove the existing well list
  • + Wells: Add the selected wells to the Master well list
  • - Wells: Remove the selected wells from the Master well list
images/Ch3_well-list-panel.png

3.5. Access projects from different operating systems

To access a cellXpress project from a different machine or operating system, first ensure that the root directory paths are set correctly, then navigate to the top-level Project root directory to locate the project that you wish to open.