UmIT | Umit is a toolbox dedicated to the analysis and management of mesoscale imaging datasets.

Dual-Camera coregistration tool

This tool is dedicated to perform the coregistration of the images from Dual-Camera Imaging systems from LabeoTech. The goal of this tool is to ensure that the output of both cameras are aligned. This documentation concerns the usage of the tool in the DataViewer app. For more information about the Dual-Camera imaging system and the acquisition software, please refer to the product's documentation.

Initial coregistration

Here we cover the steps to perform the coregistration for the first time between the data from the two cameras.

Step 1: Generate some sample recording using a high-contrast image, such as the one in the figure below.

Screenshow from LabeoTech's Imaging software showing the images from the two cameras
Step 2: Import the Data
1. Launch the DataViewer app
2. Go to File → Import Raw Data → From LabeoTech
3. Select the folder containing the sample data
4. Apply the default parameters for the data import. Once the data is imported, the Dual-Camera coregistration tool will appear:
  
  Coregistration tool interface during first time execution of the coregistration
Step 3: Execute the coregistration. Click on "Run Coregistration" to execute the coregistration on the sample data. At the end of the coregistration, open one of the channels from the camera #2 for validation

Coregistration validation

In order to validate if the coregistration worked. Go to Utilities → OiS Dual Cam Coregistration:

dual-cam-coregistration_tool_fig3
Dual-Camera coregistration tool interface showing the result of the coregistration

Use the View mode FalseColor overlay to facilitate the visualization of the registered images.

Here are some examples of a good and poor quality registration:

dual-cam-coregistration_tool_fig1
Examples of good and bad coregistrations in FalseColor view mode

How to redo the coregistration

If the first coregistration yielded an unsatisfactory result, one can redo it. To do so, delete the Geometric transformation file by clicking on the Discard button. The Geometric transformation file will be first copied to a backup file and will be deleted. Once the Geometric transformation file deleted, one can redo the coregistration by following the steps 1-3 shown in the Initial coregistration section.

To restore the backup file, click on Recover from backup button.

Note
The Geometric transformation file is located at the LabeoTech default folder ..\USER\Documents\LabeoTech\Config\umIT\tformFiles.

To access the folder, click on Show in folder button.

Automatic coregistration

The Data import function run_ImagesClassification will look for the Geometric transformation file inside the labeotech folder and will automatically apply the coregistration in all subsequent data import processes as long as the file coreg2cam_tform.mat exists. At the end of the data import process, a copy of the Geometric transformation matrix will be stored in the Save directory along with the imported .dat files.