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32 results for “Ptychography”
Overcoming information reduced data and experimentally uncertain parameters in ptychography with regularized optimization
<p>These are the datasets used for the publication <a href="https://arxiv.org/abs/2005.01530">https://arxiv.org/abs/2005.01530</a>. The bin files are the actual data, and the other files are the configuration files used to generate the datasets.</p> <p>In more detail, the Forward_Params*.cnf files were used in combination with FDES (<a href="https://doi.org/10.1016/j.ultramic.2015.07.005">https://doi.org/10.1016/j.ultramic.2015.07.005</a>) to generate diffraction patterns.</p> <p>The Reconstruction_Params*.cnf files were used with the code outlined in the main publication to generate the simulated results.</p> <p>The Simulation*.bin files are the raw simulated CBEDs, stored in a binary format. The eCount portion of the filename corresponds to the Poissonian statistics applied to simulate real data. The ground truth file is upsampled, with larger diffraction pattern sizes, while the eCountInf has infinite dose, and therefore no noise.</p> <p>If you want more information, please contact the corresponding author of the publication, at vandenbroek@physik.hu-berlin.de. </p>
Nanoscale Crystal Grain Characterization via Linear Polarization X-ray Ptychography: Raw data
<p>File Description:</p> <p>energy_rot1.dat, energy_rot2.dat</p> <p>List of energies that were taken in the spectroscopy scans of two sample orientations. Unit is KeV.</p> <p> </p> <p>P5_rot1_amp.tif, P5_rot2_amp.tif:</p> <p>Tiff stacks of absorption images of the sample scanned across Vanadium K-edge at two perpendicular orientations relative to beam polarization. Pixel values are in range of [0,20000], which equal [Normalized transmission]*20000.</p> <p> </p> <p>P5_rot1_phase.tif, P5_rot2_phase.tif:</p> <p>Tiff stacks of phase images of the sample scanned across Vanadium K-edge at two perpendicular orientations relative to beam polarization. Pixel values equal [Real part of refractive index(Delta)]*[Factor]*10000, the factor is given in separate files.</p> <p> </p> <p>delta_factor_rot1.dat, delta_factor_rot2.dat</p> <p>List of factors to calculate delta values from phase images for each energy. The factor has no unit.</p>
"An efficient ptychography reconstruction strategy through fine-tuning of large pre-trained deep learning model" train and test data
<ul><li>Model for the article "An efficient ptychography reconstruction strategy through fine-tuning of large pre-trained deep learning model".</li><li>The .pth file is the pre-trained PtyNet-S model and the fine-tuned PtyNet-B model.</li><li>Please contact panxy@ihep.ac.cn if you have any questions.</li></ul>
Achieving sub-0.5-Angstrom resolution ptychography in an uncorrected electron microscope
<p><strong>Abstract:</strong> Sub-angstrom resolution has long been limited to aberration-corrected electron microscopy, where it is a powerful tool for understanding the atomic structure and properties of matter.<span> </span><span> </span>Here, we demonstrate electron ptychography in an uncorrected scanning transmission electron microscope (STEM) with deep sub-angstrom spatial resolution down to 0.44 Ångstrom, exceeding the conventional resolution of aberration-corrected tools and rivaling their highest ptychographic resolutions. Our approach, which we demonstrate on twisted 2D materials in a widely-available commercial microscope, far surpasses prior ptychographic resolutions (1 to 5 Ångstroms) of uncorrected STEMs. We further show how geometric aberrations can create optimized, structured beams for dose-efficient electron ptychography. Our results demonstrate that expensive aberration correctors are no longer required for deep sub-angstrom resolution.</p>
Raw data for "Adaptive multi-beam X-ray ptychography"
Open the record for dataset details and reuse information.
X-ray dataset for "Illumination improvements for high-resolution ptychography"
<p>We provide X-ray ptychography datasets used for publication "Illumination improvements for high-resolution ptychography"</p> <p>The provided datasets are stored in Matlab MAT files and they contain:<br> measured_intensities uint16 - photon counts measured by a 2D hybrid-pixel detector in every scanning position <br> probe_positions double - relative probe position already converted to units of the real-space pixel shift<br> detector_mask logical - mask which is true for good pixel and false for ignored (bad or missing) pixels<br> initial_probe complex double - initial estimate of the reconstruction probe</p> <p>The pixel size for the FCC_particle datasets is 27.43nm and for the siemens_star datasets it is 9.97x14.16nm</p> <p> </p>
A semi-implicit relaxed Douglas-Rachford algorithm (sDR) for Ptychography
<p>Alternating projection based methods, such as ePIE and rPIE, have been used widely in ptychography. However, they only work well if there are adequate measurements (diffraction patterns); in the case of sparse data (i.e. fewer measurements) alternating projection underperforms and might not even converge. In this paper, we propose semi-implicit relaxed Douglas-Rachford (sDR), an accelerated iterative method, to solve the classical ptychography problem. Using both simulated and experimental data, we show that sDR improves the convergence speed and the reconstruction quality relative to extended ptychographic iterative engine (ePIE) and regularized ptychographic iterative engine (rPIE). Furthermore, in certain cases when sparsity is high, sDR converges while ePIE and rPIE fail or encounter slow convergence. To facilitate others to use the algorithm, we post the Matlab source code of sDR on a public website (www.physics.ucla.edu/research/imaging/sDR) and data con zenodo. We anticipate that this algorithm can be generally applied to the ptychographic reconstruction of a wide range of samples in the physical and biological sciences.</p>
Example far-field Ptychography Data from ESRF/ID16A for the PtyPy Tutorials : the Siemens Star
<p>Experimental ptychography data collected at the beamlines ID16A at the ESRF. The purpose of this data deposit is to provide relevant experimental ptychography data for a comprehensive collection of tutorials for the PtyPy software framework.</p>
X-ray beam characterization of an aberration-corrected pair of planar nanofocusing X-ray lenses with ptychography
<p>This data set is split over two zip archives. Each archive contains a scanning coherent X-ray diffraction (ptychography) data set recorded at an X-ray energy of 18 keV. A crossed pair of planar nanofocusing X-ray lenses (NFL) made out of silicon is used to focus the beam and scan a Siemens star test sample. Each data set includes a configuration file and scan position file. In addition, the final result of the obtained ptychographic reconstruction is included.</p><p><strong>Description of the two data sets:</strong></p><ul><li>scan_00033: X-ray beam characterization of the NFL. On this data set the design of the refractive phase correctors was based upon.</li><li>scan_00077: X-ray beam characterization of the NFL with refractive phase corrector milled to the silicon lens by focused ion-beam milling.</li></ul><p><strong>Additional information:</strong></p><p>The diffraction patterns can be found in the 'eiger4m_01' folder. They are split up over multiple h5 files and located in the group '/entry/data/data'. The assignment of diffraction patterns to scan positions can be found in the positions.txt file. All relevant input parameters for ptychography are located in the 'input' group in the ptycho.conf files. The reconstruction results are in the European Data Format (EDF).</p><p><strong>The data set has been published in:</strong></p><p>F. Seiboth, A. Schropp, M. Lyubomirskiy, W. Wang, A. Jahn, S. Kulkarni, T. F. Keller, and C. G. Schroer, "On-chip aberration correction for planar nanofocusing x-ray lenses by focused ion-beam milling," Applied Physics Letters <strong>122</strong>(24), (2023).</p>
Replication data for "Single-shot X-ray ptychography as a structured illumination method"
<p>Replication data for "Single-shot X-ray ptychography as a structured illumination method," published in Optics Letters on January 15, 2025 at <a href="https://doi.org/10.1364/OL.545836">https://doi.org/10.1364/OL.545836</a>. The author's accepted manuscript is available on the arXiv at <a href="https://doi.org/10.48550/arXiv.2410.19197">https://doi.org/10.48550/arXiv.2410.19197</a>.</p>
Raw data for "Multimodal imaging of cubic Cu2O@Au nanocage formation via galvanic replacement using X-ray ptychography and nano diffraction"
<p><strong>Raw data for "Multimodal imaging of cubic Cu2O@Au nanocage formation via galvanic replacement using X-ray ptychography and nano diffraction"</strong></p> <p>The file "raw_data_ptychography_waxs.zip" contains one HDF5 archive for each scan. The archives are structured as follows:</p> <ul> <li>section experiment: <ul> <li>identifiers of the lightsource, beamline, beamtime, session number, and scan number</li> </ul> </li> <li>section measured: <ul> <li>N diffraction patterns of size 512x512 px used for ptychography</li> <li>N WAXS patterns of size 514x1030 px</li> <li>N scan positions in mm</li> <li>one detector mask of size 512x512 px used for ptychography</li> <li>one detector mask of size 514x1030 px used for WAXS</li> <li>slice separation in mm for multi slice reconstruction</li> </ul> </li> <li>section parameters: <ul> <li>distance between sample and forward detector (ptychography) in mm</li> <li>pixel size of forward detector (ptychography) in mm</li> <li>photon energy in keV</li> <li>cropping of diffraction patterns in px used for ptychographic reconstruction</li> </ul> </li> </ul> <p>The following lists show the scan numbers with their corresponding reaction times and slice separations for the in situ series recorded during growth of Cu<sub>2</sub>O nanocubes, as well as galvanic replacement with Au measured out of focus and in focus.</p> <p>Growth of Cu<sub>2</sub>O nanocubes:</p> <table> <tbody> <tr> <td><strong>scan number</strong></td> <td><strong>slice distance, mm</strong></td> <td><strong>reaction time, h</strong></td> </tr> <tr> <td>179</td> <td>1</td> <td>1.58</td> </tr> <tr> <td>185</td> <td>1</td> <td>3.59</td> </tr> <tr> <td>191</td> <td>1</td> <td>4.78</td> </tr> <tr> <td>192</td> <td>1</td> <td>5.21</td> </tr> <tr> <td>193</td> <td>1</td> <td>5.64</td> </tr> <tr> <td>194</td> <td>1</td> <td>6.08</td> </tr> <tr> <td>195</td> <td>1</td> <td>6.51</td> </tr> <tr> <td>196</td> <td>1</td> <td>6.94</td> </tr> <tr> <td>197</td> <td>1</td> <td>7.37</td> </tr> <tr> <td>198</td> <td>1</td> <td>7.81</td> </tr> <tr> <td>199</td> <td>1</td> <td>8.24</td> </tr> <tr> <td>200</td> <td>1</td> <td>8.67</td> </tr> <tr> <td>201</td> <td>1</td> <td>9.10</td> </tr> <tr> <td>202</td> <td>1</td> <td>9.53</td> </tr> <tr> <td>203</td> <td>1</td> <td>9.97</td> </tr> <tr> <td>204</td> <td>1</td> <td>10.41</td> </tr> <tr> <td>205</td> <td>1</td> <td>10.86</td> </tr> <tr> <td>207</td> <td>0.96</td> <td>11.53</td> </tr> <tr> <td>208</td> <td>0.94</td> <td>11.96</td> </tr> <tr> <td>209</td> <td>0.92</td> <td>12.41</td> </tr> <tr> <td>210</td> <td>0.9</td> <td>12.85</td> </tr> <tr> <td>211</td> <td>0.88</td> <td>13.29</td> </tr> <tr> <td>212</td> <td>0.86</td> <td>13.74</td> </tr> <tr> <td>213</td> <td>0.84</td> <td>14.19</td> </tr> <tr> <td>215</td> <td>0.8</td> <td>15.07</td> </tr> <tr> <td>216</td> <td>0.78</td> <td>15.50</td> </tr> <tr> <td>218</td> <td>0.74</td> <td>16.06</td> </tr> <tr> <td>219</td> <td>0.72</td> <td>16.50</td> </tr> <tr> <td>220</td> <td>0.7</td> <td>16.82</td> </tr> <tr> <td>221</td> <td>0.68</td> <td>17.08</td> </tr> <tr> <td>223</td> <td>0.64</td> <td>17.79</td> </tr> <tr> <td>225</td> <td>0.6</td> <td>18.53</td> </tr> </tbody> </table> <p>Galvanic replacement with Au measured out of focus:</p> <table> <tbody> <tr> <td><strong>scan number</strong></td> <td><strong>slice distance, mm</strong></td> <td><strong>reaction time, h</strong></td> </tr> <tr> <td>263</td> <td>1</td> <td>-0.53</td> </tr> <tr> <td>265</td> <td>1</td> <td>0.13</td> </tr> <tr> <td>266</td> <td>1</td> <td>0.38</td> </tr> <tr> <td>267</td> <td>1</td> <td>0.63</td> </tr> <tr> <td>268</td> <td>1</td> <td>0.89</td> </tr> <tr> <td>269</td> <td>1</td> <td>1.14</td> </tr> <tr> <td>270</td> <td>1</td> <td>1.40</td> </tr> <tr> <td>271</td> <td>1</td> <td>1.64</td> </tr> <tr> <td>272</td> <td>1</td> <td>1.90</td> </tr> <tr> <td>273</td> <td>1</td> <td>2.14</td> </tr> <tr> <td>274</td> <td>1</td> <td>2.39</td> </tr> <tr> <td>275</td> <td>1</td> <td>2.63</td> </tr> <tr> <td>276</td> <td>1</td> <td>2.87</td> </tr> <tr> <td>277</td> <td>1</td> <td>3.11</td> </tr> <tr> <td>278</td> <td>1</td> <td>3.35</td> </tr> <tr> <td>279</td> <td>1</td> <td>3.60</td> </tr> <tr> <td>280</td> <td>1</td> <td>3.84</td> </tr> <tr> <td>281</td> <td>1</td> <td>4.08</td> </tr> <tr> <td>282</td> <td>1</td> <td>4.32</td> </tr> <tr> <td>283</td> <td>1</td> <td>4.74</td> </tr> <tr> <td>284</td> <td>1</td> <td>5.15</td> </tr> <tr> <td>286</td> <td>1</td> <td>5.59</td> </tr> <tr> <td>287</td> <td>1</td> <td>6.01</td> </tr> <tr> <td>288</td> <td>1</td> <td>6.35</td> </tr> <tr> <td>289</td> <td>1</td> <td>6.74</td> </tr> <tr> <td>290</td> <td>1</td> <td>7.15</td> </tr> <tr> <td>291</td> <td>1</td> <td>7.55</td> </tr> <tr> <td>292</td> <td>1</td> <td>7.94</td> </tr> <tr> <td>293</td> <td>1</td> <td>8.35</td> </tr> <tr> <td>294</td> <td>1</td> <td>8.75</td> </tr> <tr> <td>295</td> <td>1</td> <td>9.16</td> </tr> <tr> <td>296</td> <td>1</td> <td>9.56</td> </tr> <tr> <td>297</td> <td>1</td> <td>9.96</td> </tr> </tbody> </table> <p>Galvanic replacement with Au measured in focus:</p> <table> <tbody> <tr> <td><strong>scan number</strong></td> <td><strong>slice distance, mm</strong></td> <td><strong>reaction time, h</strong></td> </tr> <tr> <td>117</td> <td>1</td> <td>0.33</td> </tr> <tr> <td>118</td> <td>1</td> <td>0.93</td> </tr> <tr> <td>119</td> <td>1</td> <td>1.51</td> </tr> <tr> <td>120</td> <td>1</td> <td>2.08</td> </tr> <tr> <td>121</td> <td>1</td> <td>2.66</td> </tr> <tr> <td>122</td> <td>1</td> <td>3.24</td> </tr> <tr> <td>123</td> <td>1</td> <td>3.87</td> </tr> <tr> <td>124</td> <td>1</td> <td>4.44</td> </tr> <tr> <td>125</td> <td>1</td> <td>5.02</td> </tr> <tr> <td>126</td> <td>1</td> <td>5.61</td> </tr> <tr> <td>127</td> <td>1</td> <td>6.19</td> </tr> <tr> <td>128</td> <td>1</td> <td>6.77</td> </tr> <tr> <td>129</td> <td>1</td> <td>7.35</td> </tr> <tr> <td>130</td> <td>1</td> <td>7.93</td> </tr> <tr> <td>131</td> <td>1</td> <td>8.50</td> </tr> </tbody> </table> <p>The files "waxs_detector_calibration_cu2o_growth.poni" and "waxs_detector_calibration_au_galvanic_replacement.poni" contain the PONI data to be used for azimuthal integration of WAXS patterns using the pyFAI library.</p> <p><strong>Ptychographic reconstructions</strong></p> <p>The file "ptychographic_reconstructions.zip" contains the ptychographic reconstructions shown in the article and supplementary information in tiff format.</p> <p>Stacks of images corresponding to time series:</p> <ul> <li>Figure 1b, 2: P06_Cu2O_growth_scans_00179-00225_entrance_window.tif</li> <li>Figure 1b, 2: P06_Cu2O_growth_scans_00179-00225_exit_window.tif</li> <li>Figure 1d, 4, 5: P06_Au_galvanic_replacement_de-focus_scans_00263-00297_exit_window.tif</li> <li>Figure 5c: P06_Au_galvanic_replacement_in-focus_scans_00117-00131_exit_window.tif</li> </ul> <p><strong>SEM and EDX</strong></p> <p>The file "SEM_EDX.zip" contains the SEM images and EDX maps shown in Figure 3 in png format. Subfolders indicate the reaction time.</p>
Automatic parameter selection for electron ptychography via Bayesian optimization
<p>Simulated data used for experimental reconstruction parameter tuning</p>
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