Automate - lucadellasantina/ObjectFinder GitHub Wiki

Batch processing allows you to perform the same operation across multiple projects automatically.

** Processing List (top panel)**

Add projects to be processed to this list, the order in which appear in the list is the order in which they will be processed.

  • Add Project Adds the selected folder to the projects list
  • Add all projects Adds every project contained inside the selected home folder
  • Remove project Removes selected project from the list. This operation does NOT alter the project files.
  • Clear all projects Removes all the projects from the list. This operation does NOT alter the projects' files.
  • Reorder project Green button on the right of the processing list move the selected project upward / downward in the priority list

Operation settings

This series of tabs allow you to define which operation will be repeated across all projects, choose the right tab corresponding to the operation you want to perform:

  • Search Detects objects in the selected image stack using common search parameters. Search can be restricted to a selected binary mask. It is important that image stacks have the same names across all projects for this operation to succeed.
  • Colocalize Performs automated colocalization analysis between two selected sets of objects or between the selected set of object and a specific binary mask.
  • Export Mask Exports a binary mask of the selected set of objects
  • Report Exports in an excel table one of the following properties of the selected set of objects: Density by depth, Nearest neighbor overlap, nearest neighbor distance.

Processing status and options (bottom panel)

  • Save results as table Checking this box will save an excel spreadsheet with the collective results of the automatic operation for those operations producing a numeric or text summary (Report tab).
  • Time scheduler when checked will enable a timer to delay the start of the automatic processing to a specific time of day. Remember to click "Batch process" to start the countdown.
  • Batch process button will start the automatic processing (or trigger the countdown) for the projects inside processing list.
  • Batch log will inform of the status of the automatic processing and will keep track of start and end times.