Confocal images were acquired using a Zeiss LSM700 (Carl Zeiss, Germany) with 10×/0.45 plan-apochromat and 40×/1.3 plan-apochromat oil objectives and laser diode lines of 405, 488, 555 and 639 nm.
Imaging was performed on a 4-channel Olympus FV1000 laser scanning confocal microscope with a 60× oil immersion objective, and with diode laser excitations at 405 nm for DAPI, 473 nm for GFP, 559 nm for Alexa 568 and 635 nm for Alexa 633.
PALM was carried out on an Olympus IX-83 microscope equipped with 405 nm, 488 nm, 561 nm and 647 nm diode lasers and an oil immersion objective (Olympus OI 150×; NA150×).
Scanning confocal images were acquired with a Zeiss 780 confocal microscope with an Argon/2 and 561nm diode laser, a 63x/1.4 Oil plan-Apochromat 44 07 62 WD 0.19 mm objective, and captured with a GaAsP high QE 32 channel spectral array detector using Zen 2010 software (Carl Zeiss, Germany).
Samples were observed with a 63×1.4 numerical aperture (NA) oil immersion objective lens, excited with a diode 561 nm, and were viewed in a Leica TCS SP2 AOBS (Leica, Heidelberg, Germany).
Three-dimensional structured illumination microscopy (3D-SIM) (Gustafsson et al., 2008) on live-cell samples was performed using an OMX V3 Blaze system (Applied Precision, GE Healthcare) (Strauss et al., 2012) equipped with a 60×/1.42 NA PlanApo oil-immersion objective (Olympus), a 488-nm diode laser with standard filter sets, and Edge sCMOS cameras (PCO).
Live cells were imaged on a 37°C environmentally controlled chamber of a Duoscan confocal microscope system (Carl Zeiss Microimaging) with a 63× NA 1.4 oil objective and a 489 nm 100 mW diode laser with a 500 550 nm bandpass filter for GFP.
In subsequent generations, soybean seeds were analyzed for seed protein and oil composition by NIR using a Perten DA7200 diode array instrument equipped with calibration equations developed by Perten in cooperation with the University of Minnesota.
Laser-induced DSBs were generated using a confocal microscope (LSM 510 Meta, Carl Zeiss) equipped with a 37°C heating chamber (Pecon, Erbach, Germany) and a 405 nm diode laser focused through a 63x/1.4 oil immersion objective.
Fluorescence microscopy was performed using the Zeiss LSM 510 Meta inverted confocal microscope equipped with a ×63/1.4 NA (numerical aperture) oil objective, multiline argon laser (488, 514 nm), DPSS (diode-pumped solid-state) laser (561 nm) and a UV diode laser (405 nm).
