scholarly journals A multi‐state occupancy model to non‐invasively monitor visible signs of wildlife health with camera traps that accounts for image quality

2021 ◽  
Author(s):  
Maureen H. Murray ◽  
Mason Fidino ◽  
Elizabeth W. Lehrer ◽  
Juniper L. Simonis ◽  
Seth B. Magle
Keyword(s):  
Image Quality ◽  
Camera Traps ◽  
Wildlife Health ◽  
Occupancy Model

scholarly journals A dynamic occupancy model for interacting species with two spatial scales

2020 ◽  
Author(s):  
Eivind Flittie Kleiven ◽  
Frederic Barraquand ◽  
Olivier Gimenez ◽  
John-André Henden ◽  
Rolf Anker Ims ◽  
...  
Keyword(s):  
Spatial Structure ◽  
Species Interactions ◽  
Spatial Scales ◽  
Species Interaction ◽  
Camera Traps ◽  
Occupancy Models ◽  
Occupancy Model ◽  
Interacting Species ◽  
Multi Scale ◽  
Extinction Probabilities

1AbstractOccupancy models have been developed independently to account for multiple spatial scales and species interactions in a dynamic setting. However, as interacting species (e.g., predators and prey) often operate at different spatial scales, including nested spatial structure might be especially relevant in models of interacting species. Here we bridge these two model frameworks by developing a multi-scale two-species occupancy model. The model is dynamic, i.e. it estimates initial occupancy, colonization and extinction probabilities - including probabilities conditional to the other species’ presence. With a simulation study, we demonstrate that the model is able to estimate parameters without bias under low, medium and high average occupancy probabilities, as well as low, medium and high detection probabilities. We further show the model’s ability to deal with sparse field data by applying it to a multi-scale camera trapping dataset on a mustelid-rodent predator-prey system. The field study illustrates that the model allows estimation of species interaction effects on colonization and extinction probabilities at two spatial scales. This creates opportunities to explicitly account for the spatial structure found in many spatially nested study designs, and to study interacting species that have contrasted movement ranges with camera traps.

scholarly journals Predicting the distribution of a rare chipmunk (Neotamias quadrivittatus oscuraensis): comparing MaxEnt and occupancy models

2020 ◽  
Vol 101 (4) ◽  
pp. 1035-1048
Author(s):  
Ian E Perkins-Taylor ◽  
Jennifer K Frey
Keyword(s):  
Species Distribution ◽  
Environmental Variables ◽  
Vegetation Type ◽  
Ecological Factors ◽  
Small Sample ◽  
Camera Traps ◽  
Model Complexity ◽  
Occupancy Models ◽  
Occupancy Model ◽  
Factors Influencing

Abstract Species distribution models (SDMs) use presence records to determine the relationship between species occurrence and various environmental variables to create predictive maps describing the species’ distribution. The Oscura Mountains Colorado chipmunk (Neotamias quadrivittatus oscuraensis) occurs in central New Mexico and is of conservation concern due to its relict distribution and threats to habitat. We previously created an occupancy model for this taxon, but were concerned that the model may not have adequately captured the ecological factors influencing the chipmunk’s distribution because of the data hungry nature of occupancy modeling. MaxEnt is another SDM method that is particularly effective at testing large numbers of variables and handling small sample sizes. Our goal was to create a MaxEnt model for the Oscura Mountains Colorado chipmunk and to compare it with our previous occupancy model for this taxon, either to strengthen our original assessment of the relevant ecological factors or identify additional factors that were not captured by our occupancy model. We created MaxEnt models using occurrence records from baited camera traps and opportunistic surveys. We adjusted model complexity using a novel method for tuning both the regularization multiplier and feature class parameters while also performing variable selection. We compared the distribution maps and variables selected by MaxEnt to the results of our occupancy model for this taxon. The MaxEnt and occupancy models selected similar environmental variables and the overall spatial pattern of occurrence was similar for each model. Likelihood of occurrence was positively related to elevation, piñon woodland vegetation type, and topographic variables associated with escarpments. The overall similarities between the MaxEnt and occupancy models increased our confidence of the ecological factors influencing the distribution of the chipmunk. We conclude that MaxEnt offers advantages for predicting the distribution of rare species, which can help inform conservation actions.

scholarly journals Shifting up a gear with iDNA: from mammal detection events to standardized surveys

2018 ◽  
Author(s):  
Jesse F Abrams ◽  
Lisa Hoerig ◽  
Robert Brozovic ◽  
Jan Axtner ◽  
Alex Crampton-Platt ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Ad Hoc ◽  
Environmental Dna ◽  
Camera Trap ◽  
Camera Traps ◽  
Occupancy Models ◽  
Imperfect Detection ◽  
Mammal Species ◽  
Occupancy Model ◽  
Cost Efficient

Invertebrate-derived DNA (iDNA), in combination with high throughput sequencing, has been proposed as a cost-efficient and powerful tool to survey vertebrate species. Previous studies, however, have only provided evidence that vertebrates can be detected using iDNA, but have not taken the next step of placing these detection events within a statistical framework that allows for robust biodiversity assessments. Here, we compare concurrent iDNA and camera-trap surveys. Leeches were repeatedly collected in close vicinity to 64 camera-trap stations in Sabah, Malaysian Borneo. We analyze iDNA-derived mammalian detection events in a modern occupancy model that accounts for imperfect detection and compare the results with those from occupancy models parameterized with camera-trap-derived detection events. We also combine leech-iDNA and camera-trap data in a single occupancy model. We found consistent estimates of occupancy probabilities produced by our camera-trap and leech datasets. This indicates that the metabarcoding of leech-iDNA method provides reasonable estimates of occupancy and can be a suitable method for studying and monitoring mammal species in tropical rainforests. However, we also show that a more extensive collection of leeches would be needed to assess mammal biodiversity with a similar robustness as with camera traps. As certain taxa were only detected in leeches, we see great potential in complementing camera-trap studies with the iDNA approach, as long as the collection of leeches follows a similar robust and standardized sampling scheme. Synthesis and applications: The approach we describe here is not restricted to the processing of leech samples, but can be used for the analysis of other iDNA and environmental DNA (eDNA) data. Our study is the first step to shift the application of e/iDNA studies from opportunistic ad-hoc collections to systematic surveys required for long-term wildlife populations and biodiversity monitoring programs.

Progress In The Practical Application Of Automated Image Analysis To Tem Negatives

1977 ◽  
Vol 35 ◽  
pp. 214-217
Author(s):  
F. A. Heckman ◽  
E. Redman ◽  
J.E. Connolly
Keyword(s):  
Image Analysis ◽  
Image Quality ◽  
Exposure Time ◽  
Image Contrast ◽  
Automated Image Analysis ◽  
Practical Application ◽  
Factors Affecting ◽  
High Image Quality ◽  
Qualitative Evidence ◽  
Comprehensive Study

In our initial publication on this subject1) we reported results demonstrating that contrast is the most important factor in producing the high image quality required for reliable image analysis. We also listed the factors which enhance contrast in order of the experimentally determined magnitude of their effect. The two most powerful factors affecting image contrast attainable with sheet film are beam intensity and KV. At that time we had only qualitative evidence for the ranking of enhancing factors. Later we carried out the densitometric measurements which led to the results outlined below.Meaningful evaluations of the cause-effect relationships among the considerable number of variables in preparing EM negatives depend on doing things in a systematic way, varying only one parameter at a time. Unless otherwise noted, we adhered to the following procedure evolved during our comprehensive study:Philips EM-300; 30μ objective aperature; magnification 7000- 12000X, exposure time 1 second, anti-contamination device operating.

Observability of Very Thick Specimen by Using Transmission Scanning Electron Microscope

1971 ◽  
Vol 29 ◽  
pp. 26-27
Author(s):  
K. Shibatomi ◽  
T. Yamanoto ◽  
H. Koike
Keyword(s):  
Electron Microscope ◽  
Image Quality ◽  
Scanning Electron Microscope ◽  
Chromatic Aberration ◽  
Image Contrast ◽  
Objective Lens ◽  
Thick Specimen ◽  
Transmission Electron ◽  
Scanning Electron

In the observation of a thick specimen by means of a transmission electron microscope, the intensity of electrons passing through the objective lens aperture is greatly reduced. So that the image is almost invisible. In addition to this fact, it have been reported that a chromatic aberration causes the deterioration of the image contrast rather than that of the resolution. The scanning electron microscope is, however, capable of electrically amplifying the signal of the decreasing intensity, and also free from a chromatic aberration so that the deterioration of the image contrast due to the aberration can be prevented. The electrical improvement of the image quality can be carried out by using the fascionating features of the SEM, that is, the amplification of a weak in-put signal forming the image and the descriminating action of the heigh level signal of the background. This paper reports some of the experimental results about the thickness dependence of the observability and quality of the image in the case of the transmission SEM.

An Environmental Wet Cell For High Voltage Electron Microscopy

1973 ◽  
Vol 31 ◽  
pp. 18-19
Author(s):  
N.J. Tighe ◽  
H.M. Flower ◽  
P.R. Swann
Keyword(s):  
Electron Microscopy ◽  
High Temperature ◽  
Image Quality ◽  
Inelastic Scattering ◽  
High Voltage ◽  
High Voltage Electron Microscopy ◽  
Voltage Electron ◽  
Environmental Cell ◽  
Water Saturated ◽  
High Temperature Gas

A differentially pumped environmental cell has been developed for use in the AEI EM7 million volt microscope. In the initial version the column of gas traversed by the beam was 5.5mm. This permited inclusion of a tilting hot stage in the cell for investigating high temperature gas-specimen reactions. In order to examine specimens in the wet state it was found that a pressure of approximately 400 torr of water saturated helium was needed around the specimen to prevent dehydration. Inelastic scattering by the water resulted in a sharp loss of image quality. Therefore a modified cell with an ‘airgap’ of only 1.5mm has been constructed. The shorter electron path through the gas permits examination of specimens at the necessary pressure of moist helium; the specimen can still be tilted about the side entry rod axis by ±7°C to obtain stereopairs.

Image quality vs data obtainment in biological electron microscopy

1986 ◽  
Vol 44 ◽  
pp. 42-43
Author(s):  
J. E. Johnson
Keyword(s):  
Electron Microscopy ◽  
Endoplasmic Reticulum ◽  
Electron Beam ◽  
Image Quality ◽  
High Speed ◽  
Early Period ◽  
Early Years ◽  
Fluorescent Screen ◽  
Embedding Medium

In the early years of biological electron microscopy, scientists had their hands full attempting to describe the cellular microcosm that was suddenly before them on the fluorescent screen. Mitochondria, Golgi, endoplasmic reticulum, and other myriad organelles were being examined, micrographed, and documented in the literature. A major problem of that early period was the development of methods to cut sections thin enough to study under the electron beam. A microtome designed in 1943 moved the specimen toward a rotary “Cyclone” knife revolving at 12,500 RPM, or 1000 times as fast as an ordinary microtome. It was claimed that no embedding medium was necessary or that soft embedding media could be used. Collecting the sections thus cut sounded a little precarious: “The 0.1 micron sections cut with the high speed knife fly out at a tangent and are dispersed in the air. They may be collected... on... screens held near the knife“.

The influence of confocal microscope design on imaging performance

1993 ◽  
Vol 51 ◽  
pp. 144-145
Author(s):  
C J R Sheppard
Keyword(s):  
Image Quality ◽  
Fluorescence Imaging ◽  
Confocal Microscope ◽  
Industrial Applications ◽  
Three Dimensions ◽  
Design Parameters ◽  
Weak Signals ◽  
Size And Shape ◽  
Imaging Performance ◽  
Fundamental Limitation

The confocal microscope is now widely used in both biomedical and industrial applications for imaging, in three dimensions, objects with appreciable depth. There are now a range of different microscopes on the market, which have adopted a variety of different designs. The aim of this paper is to explore the effects on imaging performance of design parameters including the method of scanning, the type of detector, and the size and shape of the confocal aperture.It is becoming apparent that there is no such thing as an ideal confocal microscope: all systems have limitations and the best compromise depends on what the microscope is used for and how it is used. The most important compromise at present is between image quality and speed of scanning, which is particularly apparent when imaging with very weak signals. If great speed is not of importance, then the fundamental limitation for fluorescence imaging is the detection of sufficient numbers of photons before the fluorochrome bleaches.

Assessment of extracranial-intracranial bypass in Moyamoya disease using 3T time-of-flight MR angiography: Comparison with CT angiography

VASA ◽  
2014 ◽  
Vol 43 (4) ◽  
pp. 278-283 ◽  
Author(s):  
Qian Chen ◽  
Rongfeng Qi ◽  
Xiaoqing Cheng ◽  
Changsheng Zhou ◽  
Song Luo ◽  
...  
Keyword(s):  
Image Quality ◽  
Moyamoya Disease ◽  
Mr Angiography ◽  
Time Of Flight ◽  
Consecutive Series ◽  
Tof Mra ◽  
Bypass Patency ◽  
Significant Difference ◽  
Contrast Technique ◽  
Vessel Integrity

Background: To evaluate the value of time-of-flight MR angiography (TOF MRA) for the assessment of extracranial-intracranial (EC-IC) bypass in Moyamoya disease in comparison with computed tomography angiography (CTA). Patients and methods: A consecutive series of 23 patients with Moyamoya disease were analyzed retrospectively. Twenty three patients underwent 25 procedures of extracranial-intracranial bypass. Cranial CTA was performed within one week after the surgery to assess bypass patency. Then TOF MRA was scanned within 24 h after CTA on a 3T MRI system. Using 5-point scales (0 = poor to 4 = excellent), two radiologists rated the image quality and vessel integrity of bypass for three segments (extracranial, trepanation, intracranial). Results: Image quality was high in both CTA and TOF MRA (mean quality score 3.84 ± 0.37 and 3.8 ± 0.41), without statistical difference (p = 0.66). Mean scores of TOF MRA with respect to bypass visualization were higher than CTA in the intracranial segment (p = 0.026). No significant difference of bypass visualization regarding the extracranial and trepanation segments was found between TOF MRA and CTA (p = 0.66 and p = 0.34, respectively). For the trepanation segment, TOF MRA showed pseudo lesions in 2 of all 25 cases. Conclusions: 3T TOF MRA, a non-contrast technique not exposing the patients to radiation, proved to be at least equal to CTA for the assessment of EC-IC bypass, and even superior to CTA with respect to the intracranial segment. In addition, readers should be aware of a potential overestimation showing focal pseudo lesions of the bypass at the trepanation segment in TOF MRA.

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