Table 11 |.
Parameters for generating the RNA mosaic in BuildMosaicsGUI
| Parameter name | Default value | Function |
|---|---|---|
| backgroundCorrect | none | Parameter options are ‘none’, ‘file’, and ‘median’. Decide if illumination should be flattened. If you recorded dax files of a blank illumination, select ‘file’. If you have many fields of view with randomly positioned data, you may use ‘median’ to estimate the illumination bias from the data. To skip background correction, keep the default ‘none’ |
| method | edgeBlur | Keeping the default ‘edgeBlur’ recommended. Uses a linear gradient of overlapping images regions to stitch borders. This is typically best for avoiding artificial edges. Other options include ‘mean’ - average the overlap, ‘sum’ - add the overlap, ‘last’ - use the last image and cover over what was imaged before, ‘first’ - use the first image and ignore later data |
| mosaicContrastLow | 0.1 | Contrast to use when rendering images. This fraction of the dimmest pixels will be set to zero/black |
| mosaicContrastHigh | 0.9999 | Contrast to use when rendering an image. This fraction of the brightest pixels in the image will be saturated |
| fovs | inf | “inf” default value is recommended to use all FOV in the folder. Optionally, select a subset (e.g. “[2:10,15:35]”) |
| hybs | inf | Hybridization data that will be displayed in the mosaic |
| dataType | all | Fiducial and readout data will be displayed in the mosaic |
| transpose | true | The default is ‘true’, which gives you the option to transpose tiles in creating mosaic |
| scope | autoDetect | Depending on the camera orientation, individual tiles may be flipped across the left-right and up-down axis to properly render the mosaic. In our case, the camera orientation is auto detected based on the pixel size of the raw images. Outside users will have to configure this setting in the MATLAB code to make sure that the tiles are oriented correctly. Our code within the Github link (https://github.com/BoettigerLab/ORCA-public) is commented in BuildMosaicsGUI.m to make sure the user knows where to make the appropriate changes based on their camera orientation |
| trimBorder | 10 | Remove the number of specified pixels around the border - sometimes our cameras have a bright line of pixels at the edge of the image, for reasons currently unclear. This removes them |