Configure image import

Supported organization of input images

• Single file: A single file contains all frames, detection channels and positions
• One file per channel and position: For each position, there is one file per detection channel, which contains all frames. File names must contain the user-defined channel keywords (defined in Detection Channel). For a given position, the file names should differ only by their channel keyword.
• One file per channel, position and frame: A single file corresponds to a single position, a single detection channel and a single frame. All files must have the same extension. File names must contain the user-defined channel keywords (defined in Detection Channel), the user-defined position separator, and contain the user-defined frame separator followed by the frame index. For a given position, the file names should only differ by their channel keyword and their frame index

Image calibration

Image calibration should be imported from image metadata. For .dv files, image calibration is found in the .log file (if existing).

To check image calibration has been correctly imported, open the input images of a position, hit: Ctrl + shit + P, and check pixel width/height and voxel depth.

If calibration has not been correctly imported, it can be manually set: in the Configuration tab, unfold Pre-processing for all positions and the position in which calibration should be modified, unfold Pre-processing and right click on Voxel Calibration, choose Custom calibration and set the calibration values.

• To set this change on all imported position, right-click on Pre-processing click on Select all and on Overwrite pipeline on selected positions.
• To set this change on the next imported position right-click on Pre-processing and choose Copy pipeline to template