Colocalization - lucadellasantina/ObjectFinder GitHub Wiki

ObjectFinder allows you to perform colocalization analysis on any detected set of objects.

Manual Colocalization analysis

  1. From the top list, select a set of objects to colocalize
  2. From second list from the top, select 1 or 2 image stacks to colocalize objects with
  3. Press "Colocalize Manually" button to start manual colocalization

You will be prompted with a sliced volume inspector centered to one object at the time and be asked whether the object colocalizes with the image stack displayed in a different color. Use the mouse wheel to scroll the volume. Objects will be presented to you in random order. You can save the progress to resume later using the "save" button.

Automated colocalization analysis against a binary mask

  1. From the list to the left, select a set of objects to colocalize
  2. From the list to the right, select a binary mask to colocalize objects with.
  3. Choose an overlap threshold to consider objects colocalized, either a fixed amount of voxel overlap or a constant fraction of the reference object's volume.
  4. Press "Colocalize Binary Mask"

Automated colocalization analysis of nearest neighbors

  1. Select 2 sets of objects from the top list, the first set of objects selected will be the reference objects, the second set will be the colocalizing (test) objects.
  2. Choose an overlap threshold to consider objects colocalized, either a fixed amount of voxel overlap or a constant fraction of the reference object's volume (defualt 50%)
  3. Choose whether colocalized objects centroids must be within a critical distance (default Infinite) 1 Choose whether the centroid of colocalized object must fall within the perimeter of the reference object (default disabled)
  4. Press the button "Nearest Neighbors"

Automated colocalization analysis of engulfed objects

  1. Select 2 sets of objects from the top list, the first set of objects selected will be the reference objects, the second set will be the engulfed (test) objects.
  2. Choose an overlap threshold to consider objects engulfed, either a fixed amount of voxel overlap or a constant fraction of the reference object's volume (defualt 50%)
  3. Choose whether colocalized objects centroids must be within a critical distance (default Infinite) 1 Choose whether the centroid of colocalized object must fall within the perimeter of the reference object (default disabled)
  4. Press the button "Engulfed objects"

Once the colocalization analysis is done, a new item will be added to the list of processed channels.

Optionally, you can check the box "Save colocalized objects" and "Save not colocalized objects" to create a new sets of objects representing only colocalized/non-colocalized, respectively.

Review Completed analysis (bottom panel)

Select a colocalization analysis from the processed channels list to display its info and colocalization rate.

If two channels were colocalized with the objects at the same time, a double-colocalization rate will be displayed.

If an engulfed objects colocalization was performed, the number of engulfed objects will be displayes.

  • Check Colocalized/not-Colocalized: You can manually verify colocalized and non-objects by pressing the "Check Colocalized" and "Check not Colocalized" buttons, you'll be asked to validate manually the co-localization status of each object presented to you in a random order.

  • Colocalization statistics: Plots the number of colocalized/engulfed objects

  • Save colocalization stats: Saves the colocalization table to disk

  • Remove colocalization analysis: Deletes the selected colocalization analysis from disk. This action is permanent!

  • Clear colocalization analysis list: Deletes all listed colocalization analyses from disk. This action is permanent!