diff --git a/docs/cmd.rst b/docs/cmd.rst index 430dac25..606097d4 100644 --- a/docs/cmd.rst +++ b/docs/cmd.rst @@ -22,7 +22,7 @@ The reconstruction parameters can be specified by adding respective arguments. I :: ‘-b’, ‘–box-side-length’, type=int, default=7, help=‘box side length’ - ‘-a’, ‘–fit-method’, choices=[‘mle’, ‘lq’, ‘avg’], default=‘mle’ + ‘-a’, ‘–fit-method’, choices=["mle", "lq", "lq-gpu", "lq-3d", "lq-gpu-3d", "avg"], default=‘mle’ ‘-g’, ‘–gradient’, type=int, default=5000, help=‘minimum net gradient’ ‘-d’, ‘–drift’, type=int, default=1000, help=‘segmentation size for subsequent RCC, 0 to deactivate’ ‘-bl’, ‘–baseline’, type=int, default=0, help=‘camera baseline’ @@ -36,6 +36,8 @@ drift corrected locs will be created. Note 2: Make sure to set the camera settings correctly, otherwise Photon counts are wrong plus the MLE might have problems. +Note 3: If you select one of the 3D algorithms (lq-3d or lq-gpu-3d) the programm will ask you to enter the magnification factor and the path to the 3D calibration file. + Example ^^^^^^^ This example shows the batch process of a folder, with movie ome.tifs that are supposed to be reconstructed and drift corrected with the ``lq``-Algorithm and a gradient of 4000.