Table 8 |.
Parameters for channel-to-channel drift-correction in BuildMosaicsGUI
| Parameter name | Default value | Function |
|---|---|---|
| alignContrastLow | 0.7 | This fraction of the dimmest pixels will be ignored for the alignment |
| alignContrastHigh | 0.9995 | Pixels brighter than this fraction of the brightest pixels will be saturated for the alignment |
| refHybe | 1 | The fiducial data from this hybridization round (e.g. ‘1’) will be used as the alignment reference |
| maxSize | 400 | For the coarse alignment step, the images larger than this size will be downsampled so the average dimension is this size |
| fineBox | 200 | Fine scale alignment extends this far in pixels around the center point |
| fineUpsample | 1 | Data will be upsampled by this factor to improve accuracy of fine alignment |
| maxShift | inf | The maximum number of pixels the coarse alignment may shift the image |
| gradMax | true | Boolean indicates whether or not to use the gradient of the correlation plot instead of the correlation values |
| minGrad | -inf | Minimum slope observed in the correlation map to accept a shift. To use any shift, keep default of “-inf” |
| fineMaxShift | 10 | Maximum number of pixels the fine alignment may shift the image |
| fineCenter | [0 0] | Fine scale alignment is centered at this point. If left at [0,0], the brightest region (not brightest pixel) of the image will be selected |
| showplot | true | Show plots during imaging |
| fastdisplay | true | Boolean, indicating whether display should be accelerated by downsampling. Typically limited by screen resolution; if you aren’t pausing and zooming in on the data, this should not affect quality |
| displayWidth | 500 | Image size to downsample to for fast display |
| showExtraPlot | false | As the default, correlation maps will not be displayed. Can be changed to ‘true’ to show the correlation maps, which can be useful for troubleshooting |
| minFineImprovement | 0 | If the correlation coefficient does not improve by this amount upon fine-scale alignment, reject the fine scale alignment |
| showCorrAlign | true | Shows images of before alignment, after coarse alignment, and after fine alignment. It is not recommended to change this parameter as keeping it ‘true’ allows you to visually check if the alignment is happening correctly |