Zeiss Lightsheet Z.1 Operating Manual

Contents

CHAPTER 4 - SYSTEM OPERATIONLightsheet Z.1 Left Tool Area and Hardware Control Tools Carl Zeiss02/2013 000000-1790-528 139Lateral (Fig. 222) is used to correct for linear lateral andaxial drifts, that is in all directions. Linear alignments areperformed in the x, y and z direction, when the Appliedbutton is pressed. The respective offsets (coefficients) aredisplayed in the coefficient table in the X, Y and Zcolumns, respectively (Fig. 223).For SIM, WF and SWF images, the software will usesignificant structures for performing the alignment. Youcan set a ROI and then the structure within the ROI isused. For HR (PALM) images at least one fiducial isexpected. Without a fiducial, no alignment will beperformed in this case.Affine is used to correct for linear lateral (X, Y) and axial(Z) drifts, rotational offsets in the image plane in x and y(RX, RY) as well as a 1st order stretching in the imageplane in x and y (SX, SY). The respective offsets(coefficients) are displayed in the coefficient table inthe corresponding columns (Fig. 224). The scrollbar canbe used to have access to all columns. For SIM, WF andSWF images, the software will use significant structuresfor performing the alignment. You can set a ROI andthen the structure within the ROI is used. For HR (PALM)images at least three fiducials are expected. Withoutfiducials, no alignment will be performed in this case.Parabolic is used to correct for linear lateral (X, Y) andaxial (Z) drifts as well as chromatic aberrations, where a2nd order stretching in the image plane in x (X1, X2) andy (Y1, Y2) is performed. The respective offsets(coefficients) are displayed in the coefficient table inthe corresponding columns (Fig. 225). The scrollbar canbe used to have access to all columns. Parabolic onlyworks with HR (PALM) images and is displayed only inthe Alignment mode drop down menu, when a HR(PALM) image is selected as the Input image.The calculated coefficients in the coefficient tablecan be edited by hand. The correction will beexactly performed when pressing Apply accordingto the coefficients in the coefficient table.If the Save button is pressed, the coefficient table (with the coefficients) will be saved in a .binfile. These .bin file can be reloaded by pressing the Load button via the Windows Explorer. TheLoad button becomes only active when the Fit check box is not active.Fig. 222 Alignment mode drop downmenu for selected PALM imageFig. 223 Correction table in the Lateralalignment modeFig. 224 Coefficient table in the Affinealignment modeFig. 225 Coefficient table in the Parabolicalignment mode