Accurate magnification determination for cryoEM using gold

Determining the correct magnified pixel size of single-particle cryoEM micrographs is necessary to maximize resolution and enable accurate model building. Here we describe a simple and rapid procedure for determining the absolute magnification in an electron cryomicroscope to a precision of <0.5%. We show how to use the atomic lattice spacings of crystals of thin and readily available test specimens, such as gold, as an absolute reference to determine magnification for both room temperature and cryogenic imaging. We compare this method to other commonly used methods, and show that it provides comparable accuracy in spite of its simplicity. This magnification calibration method provides a definitive reference quantity for data analysis and processing, simplifies the combination of multiple datasets from different microscopes and detectors, and improves the accuracy with which the contrast transfer function of the microscope can be determined. We also provide an open source program, magCalEM, which can be used to accurately estimate the magnified pixel size of a cryoEM dataset ex post facto.

Quantification of myocardial blood flow and myocardial flow reserve by 13N-NH3 PET/CT is not significantly affected by pixel size

PURPOSE

Myocardial blood flow (MBF) and myocardial flow reserve (MFR) are measurable by ¹³N-NH₃ positron emission tomography (PET). MFR, which is the ratio of MBF under adenosine stress to MBF at rest, is prognostically valuable. The ASNC imaging guidelines/SNMMI procedure standards recommend using 2-3 mm pixels, and pixel size does differ between institutions. We sought to evaluate the effects of pixel sizes on the quantitative values calculated from ¹³N-NH₃ PET images.

METHODS

Thirty consecutive patients with ischemic heart disease who underwent ¹³N-NH₃ PET were retrospectively enrolled. Dynamic images were quantified using PMOD's cardiac PET analysis tool (pixel sizes: 3.18, 2.03, and 1.59 mm). MBF under adenosine stress, MBF at rest, and MFR for the right coronary artery (RCA) region, left anterior descending artery region, and left circumflex coronary artery branch region innervation regions were calculated at each pixel size and compared.

RESULTS

Quantitative values did not significantly differ according to pixel size in any of the regions. However, MFR values for the RCA fluctuated the most. Ischemic and non-ischemic regions remained visually discernible in qualitative images, with no variation in quantitative values, regardless of pixel size.

CONCLUSIONS

Quantitative values were not significantly affected by pixel sizes within the recommended range of 2-3 mm. Values for the RCA region may have been overestimated, but this was true for all pixel sizes.

Performance of 3D diamond detectors in small field dosimetry: The impact of pixel size

PURPOSE

Small photon beams used in radiotherapy techniques have inherent characteristics of charge particle disequilibrium and high-dose gradient making accurate dosimetry for such fields very challenging. By means of a 3D manufacturing technique, it is possible to create arrays of pixels with a very small sensitive volume for radiotherapy dosimetry. We investigate the impact of 3D pixels size on absorbed dose sensitivity, linearity of response with dose rate, reproducibility and beam profile measurements.

METHODS

Diamond detectors with different pixel sizes have been produced in the 3DOSE experiment framework. To investigate the pixels size impact, they were tested using an Elekta Synergy LINAC. Dose rate dependence, absorbed dose sensitivity, reproducibility and beam profile measurement accuracy have been investigated and compared with PTW 60019 and IBA SFD reference dosimeters.

RESULTS

All of the 3D pixels had a linear and reproducible response to the dose rate. The sensitivity of a pixel decreases with its size, although even the smallest pixel has a high absorbed dose sensitivity (15 nC/Gy). The penumbra width measured with the smallest pixel size was consistent with the PTW microDiamond and differed by 0.2 mm from the IBA SFD diode.

CONCLUSIONS

The study demonstrates that variation in pixel size do not affect the linearity of response with dose rate and the reproducibility of response. Due to the 3D geometry, the absorbed dose sensitivity of the detector remains high even for the smallest pixel, furthermore the pixel size was demonstrated to be of fundamental importance in the measurement of beam profiles.

Identification and visualisation of microplastics/ nanoplastics by Raman imaging (ii): Smaller than the diffraction limit of laser?

We recently reported (Sobhani et al., 2020) that when a confocal Raman microscope imaged a nanoplastic with the diameter of 100 nm, the imaging lateral size was 300-400 nm, due to the diffraction limit of the laser spot. In this study, we examine the lateral intensity distribution of the Raman signal emitted by nanoplastics (diameters ranging ∼30-600 nm) within the excitation laser spot. We find that the Raman emission intensity, similar to the excitation power density distributed within a laser spot, also follows a lateral Gaussian distribution. To image and visualise individual nanoplastics, we (i) decrease the mapping pixel size, in a hope to generate an image with high-resolution and simultaneously to pick up items from the "blind point". We can then either (ii) offset the colour to intentionally image only the high-intensity portion of the Raman signal (emitted from the centre of the laser spot), to localise the exact position of the nanoplastic; or (iii) categorise the imaged nanoplastics to different groups via their Raman intensity, to simultaneously and separately visualise large nanoplastics/strong Raman signals, medium nanoplastics and small nanoplastics, in an effort to avoid the shielding and overlooking of weak signals. We (iv) also cross-check multi-images simultaneously mapped at two or three characteristic peaks via either a logic-OR or a logic-AND algorithm. Thus the imaging uncertainty can be significantly reduced from a statistical point of view.