Dentist

Introduction

The application takes as its starting point a collection of single-plane images, possibly in multiple channels, that tile a large field of view in a microscope. It is named "Dentist" for historical reasons.

Dentist analyzes the stitched-together image to find cells using a nuclear stain and RNA spots. It assigns RNA spots to cells, and lets you visualize the results using the dentistGUI.

Usage

You must have installed rajlabimagetools. Dentist is a part of rajlabimagetools.

Dentist needs files named according to our normal position file prefixes per channel, rather than the Scan Slide wave and file numbers. Before using dentist, call:

>> RenameFiles
% assign the corresponding names to each wavelength from the following options:
% trans
% dapi
% alexa
% tmr
% cy
% gfp
% nir

Navigate in matlab to the directory with image data. Initialize the configuration file:

>> dentist.initialize(Nrows, Ncolumns);

Where Nrows and Ncolumns are the number of rows and columns making up the tiling image.

Then specify the order in which the images were taken (for example, left-to-right, then top-to-bottom, with or without snaking), using the layout selector GUI:

>> dentist.setLayout();

Images in a tiling array usually overlap. Run the following to open a GUI that helps you set how much the images overlap, in pixels:

>> dentist.setImageOverlap();

If it turns out that the tiling is quite skewed, you can click the red "Shift GUI" button which will launch the shiftGUI. Documentation for operating this GUI can be found here - skip the section about launching the GUI

To now process the images, finding spots and centroids (cells) and matching spots to centroids, run:

>> dentist.processImages();

This may take some time, and will save the results to your working directory.

Once done, you can launch the GUI with:

>> controls = dentist.launchGUI();

Use the save button to save any changes to the data - only changes to the thresholds or to the deletions merit saving.

the controls structure returned by the GUI launcher contains references to many objects that can be used to control or query GUI state and objects that can be queried for actual data. For more info on any of these objects, use the moreinfo command.

When done, close the window, and clear the controls variable from your workspace.

To access the spots and centroids for other uses in Matlab, such as exporting to a text file, use:

>> spotsAndCentroids = dentist.load();

which creates an object in your workspace that you can query for the list and locations of centroids, as well as how many RNA spots in each color are assigned to them.