Automatic cell segmentation by adaptive thresholding (ACSAT) for large-scale calcium imaging datasets

Advances in calcium imaging have made it possible to record from an increasingly larger number of neurons simultaneously. Neuroscientists can now routinely image hundreds to thousands of individual neurons. An emerging technical challenge that parallels the advancement in imaging a large number of individual neurons is the processing of correspondingly large datasets. One important step is the identification of individual neurons. Traditional methods rely mainly on manual or semimanual inspection, which cannot be scaled for processing large datasets. To address this challenge, we focused on developing an automated segmentation method, which we refer to as automated cell segmentation by adaptive thresholding (ACSAT). ACSAT works with a time-collapsed image and includes an iterative procedure that automatically calculates global and local threshold values during successive iterations based on the distribution of image pixel intensities. Thus, the algorithm is capable of handling variations in morphological details and in fluorescence intensities in different calcium imaging datasets. In this paper, we demonstrate the utility of ACSAT by testing it on 500 simulated datasets, two wide-field hippocampus datasets, a wide-field striatum dataset, a wide-field cell culture dataset, and a two-photon hippocampus dataset. For the simulated datasets with truth, ACSAT achieved >80% recall and precision when the signal-to-noise ratio was no less than ∼24 dB.DP2 NS082126 - NINDS NIH HHSPublished versio

Uplink Linear Receivers for Multi-cell Multiuser MIMO with Pilot Contamination: Large System Analysis

Base stations with a large number of transmit antennas have the potential to serve a large number of users at high rates. However, the receiver processing in the uplink relies on channel estimates which are known to suffer from pilot interference. In this work, making use of the similarity of the uplink received signal in CDMA with that of a multi-cell multi-antenna system, we perform a large system analysis when the receiver employs an MMSE filter with a pilot contaminated estimate. We assume a Rayleigh fading channel with different received powers from users. We find the asymptotic Signal to Interference plus Noise Ratio (SINR) as the number of antennas and number of users per base station grow large while maintaining a fixed ratio. Through the SINR expression we explore the scenario where the number of users being served are comparable to the number of antennas at the base station. The SINR explicitly captures the effect of pilot contamination and is found to be the same as that employing a matched filter with a pilot contaminated estimate. We also find the exact expression for the interference suppression obtained using an MMSE filter which is an important factor when there are significant number of users in the system as compared to the number of antennas. In a typical set up, in terms of the five percentile SINR, the MMSE filter is shown to provide significant gains over matched filtering and is within 5 dB of MMSE filter with perfect channel estimate. Simulation results for achievable rates are close to large system limits for even a 10-antenna base station with 3 or more users per cell.Comment: Accepted for publication in IEEE Transactions on Wireless Communication

MEMS-Based Terahertz Photoacoustic Chemical Sensing System

Advancements in microelectromechanical system (MEMS) technology over the last several decades has been a driving force behind miniaturizing and improving sensor designs. In this work, a specialized cantilever pressure sensor was designed, modeled, and fabricated to investigate the photoacoustic (PA) response of gases to terahertz (THz) radiation under low-vacuum conditions associated with high-resolution spectroscopy. Microfabricated cantilever devices made using silicon-on-insulator (SOI) wafers were tested in a custom-built test chamber in this first ever demonstration of a cantilever-based PA chemical sensor and spectroscopy system in the THz frequency regime. The THz radiation source was amplitude modulated to excite acoustic waves in the chamber, and PA molecular spectroscopy of a gas species was performed. An optical measurement technique was used to evaluate the PA effect on the cantilever sensor; a laser beam was reflected off the cantilever tip and through an iris to a photodiode. As the cantilever movement deflected the laser beam, the beam was clipped by an iris and generated the PA signal. Experimental data indicated a predominantly linear response in signal amplitude from the photodiode measurement technique, which directly correlated to measured cantilever deflections. Using the custom-designed PA chamber and MEMS cantilever sensor, excellent low-pressure PA spectral data of methyl cyanide (CH3CN) at 2 to 40 mTorr range has been obtained. At low chamber pressures, the sensitivity of our system was 1.97 × 10−5 cm−1 and had an excellent normalized noise equivalent absorption (NNEA) coefficient of 1.39 × 10−9 cm−1 W Hz-½ using a 0.5 s signal averaging time