Towards Optimal Image Stitching for Virtual Microscopy

In this paper we present an image stitching method based on dynamic programming and describe its application to automated slide acquisition for Virtual Microscopy (VM). Given a large number of fields of view (FOVs) acquired from a single microscope slide, we composite these images into a single large 'virtual slide' image. The location of each FOV is determined using a new algorithm based on dynamic programming. We compare the performance of the proposed algorithm to an existing greedy algorithm. In a visual trial it is shown that the new algorithm provides a significant improvement in perceived image quality at image boundaries compared to the existing algorithm

Elliptical Distance Transforms And Object Splitting

The classical morphological method to separate fused objects in binary images is to use the watershed transform on the complement of the distance transform of the binary image. This method assumes roughly disk-like objects and cannot separate objects when they are fused together beyond a certain point. In this paper we revisit the issue by assuming that fused objects are unions of ellipses rather than mere disks. The problem is recast in terms of finding the constituent primary grains given a boolean model of ellipses. To this end, we modify the well-known pseudo-Euclidean distance transform algorithm to generate arbitrary elliptical distance transforms to reduce the dimension of the problem and we present a goodness-of-fit measure that allows us to select ellipses. The results of the methods are given on both synthetic sample boolean models and real data

Spatially Resolved Spitzer-IRS Spectroscopy of the Central Region of M82

We present high spatial resolution (~ 35 parsec) 5-38 um spectra of the central region of M82, taken with the Spitzer Infrared Spectrograph. From these spectra we determined the fluxes and equivalent widths of key diagnostic features, such as the [NeII]12.8um, [NeIII]15.5um, and H_2 S(1)17.03um lines, and the broad mid-IR polycyclic aromatic hydrocarbon (PAH) emission features in six representative regions and analysed the spatial distribution of these lines and their ratios across the central region. We find a good correlation of the dust extinction with the CO 1-0 emission. The PAH emission follows closely the ionization structure along the galactic disk. The observed variations of the diagnostic PAH ratios across M82 can be explained by extinction effects, within systematic uncertainties. The 16-18um PAH complex is very prominent, and its equivalent width is enhanced outwards from the galactic plane. We interpret this as a consequence of the variation of the UV radiation field. The EWs of the 11.3um PAH feature and the H_2 S(1) line correlate closely, and we conclude that shocks in the outflow regions have no measurable influence on the H_2 emission. The [NeIII]/[NeII] ratio is on average low at ~0.18, and shows little variations across the plane, indicating that the dominant stellar population is evolved (5 - 6 Myr) and well distributed. There is a slight increase of the ratio with distance from the galactic plane of M82 which we attribute to a decrease in gas density. Our observations indicate that the star formation rate has decreased significantly in the last 5 Myr. The quantities of dust and molecular gas in the central area of the galaxy argue against starvation and for negative feedback processes, observable through the strong extra-planar outflows.Comment: 15 pages, 12 figures, 3 tables, ApJ, emulateap

Globally optimal 3D image reconstruction and segmentation via energy minimisation techniques

This paper provides an overview of a number of techniques developed within our group to perform 3D reconstruction and image segmentation based of the application of energy minimisation concepts. We begin with classical snake techniques and show how similar energy minimisation concepts can be extended to derive globally optimal segmentation methods. Then we discuss more recent work based on geodesic active contours that can lead to globally optimal segmentations and reconstructions in 2D. Finally we extend the work to 3D by introducing continuous flow globally minimal surfaces. Several applications are discussed to show the wide applicability and suitability of these techniques to several difficult image analysis problems

IRAC Observations of M81

IRAC images of M81 show three distinct morphological constituents: a smooth distribution of evolved stars with bulge, disk, and spiral arm components; a clumpy distribution of dust emission tracing the spiral arms; and a pointlike nuclear source. The bulge stellar colors are consistent with M-type giants, and the disk colors are consistent with a slightly younger population. The dust emission generally follows the blue and ultraviolet emission, but there are large areas that have dust emission without ultraviolet and smaller areas with ultraviolet but little dust emission. The former are presumably caused by extinction, and the latter may be due to cavities in the gas and dust created by supernova explosions. The nucleus appears fainter at 8 um than expected from ground-based 10 um observations made four years ago.Comment: ApJS in press (Spitzer special issue); 15 pages, 3 figures. Changes: unused references removed, numbers and labels in Table 1 change

A Spitzer Unbiased Ultradeep Spectroscopic Survey

We carried out an unbiased, spectroscopic survey using the low-resolution module of the infrared spectrograph (IRS) on board Spitzer targeting two 2.6 square arcminute regions in the GOODS-North field. IRS was used in spectral mapping mode with 5 hours of effective integration time per pixel. One region was covered between 14 and 21 microns and the other between 20 and 35 microns. We extracted spectra for 45 sources. About 84% of the sources have reported detections by GOODS at 24 microns, with a median F_nu(24um) ~ 100 uJy. All but one source are detected in all four IRAC bands, 3.6 to 8 microns. We use a new cross-correlation technique to measure redshifts and estimate IRS spectral types; this was successful for ~60% of the spectra. Fourteen sources show significant PAH emission, four mostly SiO absorption, eight present mixed spectral signatures (low PAH and/or SiO) and two show a single line in emission. For the remaining 17, no spectral features were detected. Redshifts range from z ~ 0.2 to z ~ 2.2, with a median of 1. IR Luminosities are roughly estimated from 24 microns flux densities, and have median values of 2.2 x 10^{11} L_{\odot} and 7.5 x 10^{11} L_{\odot} at z ~ 1 and z ~ 2 respectively. This sample has fewer AGN than previous faint samples observed with IRS, which we attribute to the fainter luminosities reached here.Comment: Published in Ap