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Diffusion Spots And Surface Distance Map XTension (spot-count) Browse

xt-distance-maps/README.md
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XT Spots To Surfaces Distances
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## 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
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