XT Spots To Surfaces Distances

Users

Maxime Ayer, Polymers Laboratory LP Maria Donaldson, Oricchio Group

Description

Imaris XTension: Interface for detecting spots, surfaces and providing the distance of each spot to each surface via generation of a euclidean distance map.

Interface

Each tab in the interface represents one channel. With each channel, the user decides what to do (Detect spots, surfaces or do nothing). After the parameters are set and tested, the user can then use the right-hand buttons.

Refresh

Re-reads the current Imaris Dataset and refreshes the number of channels, as needed

Detect All

Runs the full detection of spots and surfaces on the dataset and ensures that the dataset is converted to 32/bit before that This is a necessary step, always use the Detect All Button

Analyze

Runs the analysis by splitting the spots into one new spots object per surface and outputs the result as a Matlab Table that is then saved in XLS format. The table is saved in the same folder as the image and either

• Has the name of the current image if Append Results is unchecked
• Is called *dist-analysis.xls* if Append Results is checked

Table Columns

Image Name Spot Name Distance Map Channel Spot ID Surface ID Sub-Surface ID (Cell) Spot X Spot Y Spot Z Spot Distance Normalized Distance from Edge Longest Distance in suface Intensity Mean Ch#

Absolute distances are negative when INSIDE the surfaces and positive when OUTSIDE

Batch Process

Request a folder and runs the analysis with the given parameters on all images in the folder. Please note that this is known to cause instability in Imaris.

Saving and Restoring Settings

Settings can be saved and loaded using the provided buttons