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In Situ Transmission Electron Microscopy Data of Dislocations in Imperfectly Attached PbTe Nanocrystal Pairs

Cite this dataset

Ondry, Justin; Hauwiller, Matthew; Alivisatos, A. Paul (2018). In Situ Transmission Electron Microscopy Data of Dislocations in Imperfectly Attached PbTe Nanocrystal Pairs [Dataset]. Dryad.


Dataset containing high resolution transmission electron microscopy data of imperfectly attached PbTe nanocrystals.  The data contains High Resolution TEM timeseries of images showing the annealing of of well defined b=a/2[110] edge dislocations in PbTe nanocrystal pairs viewed down the<001> zone axis.  Depending on the attachment facets of the particles, the dislocations anneal out at different rates.  In addition we performed geometric phase analysis on the images to visualize the strain fields surrounding the dislocation cores.  The raw image series, as well as drift corrected image series and all strain and rotation maps from geometric phase analysis are included in this dataset.  Further overlays of dislocation positions determined by geometric phase analysis overlaid on raw images are included to show the validity of dislocaiton tracking. Simple scripts used to analyze dislocation positions and overlay strain fields with TEM images for visualization and are included in this dataset.  


Nanocrystal synthesis: PbTe nanocrystals were synthesized based on modified methods from Zhu et. al.73 1.0 M TOP-Te was prepared by dissolving tellurium shot in TOP in an argon glovebox (<1 ppm O2 and H2O) at room temperature for ~36 hours.  Next, 900 mg PbO, 7.56 g OA, 16 g ODE were loaded in a 3-neck round bottom flask and heated under vacuum on a Schlenk line at 100C for 1 hour to complex lead oleate and dry the solution.  The flask was refilled with argon (ultrapure <1ppm O2) 3X and heated to 120°C. 2 ml of the 1.0 M TOP-Te solution was injected and the nanocrystals were allowed to grow for 10 min at 120 °C.  The reaction was quenched by quickly cooling to room temperature using a water bath.  The nanocrystals were cannula transferred to a Schlenk flask and transferred to an argon glovebox.  The nanocrystals were washed 3X by precipitating them with excess acetone, centrifuging and dissolving the resulting pellet in toluene.  The sample were stored in an argon glovebox.  It was found that pristine unoxidized surfaces were necessary for ligand displacement mediated attachment.

TEM sample preparation: Graphene coated TEM grids were prepared by direct transfer of 3-5 layer graphene onto holey quatifoil TEM grids.74  PbTe particles sandwiched between graphene sheets where prepared based on modified methods for making graphene veils and sandwitches.75 Briefly, in a glovebox a small droplet of dilute PbTe nanocrystals in toluene was dropped on a graphene coated TEM grid and the droplet was allowed to dry. A second graphene coated TEM grid was placed on top and a droplet of toluene or orthodichlobenzene (ODCB) was placed on the sandwich.  This assembly was covered with a glass dish and the solvent was allowed to slowly evaporate for several hours to seal the sample between the graphene.  The sample was taken out of the glovebox and quickly (~3min) transferred to the TEM column.

TEM imaging: TEM imaging was performed on a FEI Tecnai T20 S-TWIN TEM operating at 200kV with a LaB6 filament.  Images were taken near Scherzer focus which resulted in dark atom contrast for this crystal thickness.  Timeseries of TEM images were collected with a Gatan Orius SC200 using a custom digital micrograph script with full 2048x2048 pixel readout, at a nominal magnification of 400kX resulting in a pixel resolution of 0.13Å/pixel, an exposure time of 1s, and a readout time of 1.4s yielding a framerate of 0.4 fps.  Since the defect dynamics were beam initiated, care was taken to minimize electron dose prior to imaging. Searching was performed with a spread beam, then once a suitable defective nanoparticle was found, a custom Digital Micrograph script was used to condense the beam to reproducibly return to the same dose rate within a session for each movie acquisition. We estimate a dose rate of ~4000 e-2s was used for all data collected.

Image Analysis: The movies were drift corrected using a cross correlation method using the raw images as inputs and manually checked and corrected where necessary (Stack Alignment, Dave Mitchell's DigitalMicrograph™ Scripting Website, The geometric phase analysis (GPA) and all other analysis was performed with the raw but drift corrected unrotated images from our CCD camera to avoid introducing artifacts. Geometric phase analysis was performed using the GPA tool contained in the FRWRtools plugin (  for Gatan Digital Micrograph.  The (200) and (020) peaks were used for analysis with a reference lattice with a and b parameters of 3.09Å with a 90° angle between the two, a resolution of 0.7 nm and a smoothing of 0.6 with a symmetric strain matrix.

Usage notes

See readme files in the dataset


United States Department of Energy, Award: KC3103