Accepted or In Press



Pei, J, L Wang, X Wang, Z Niu, M Kelly, X Song, N Huang, J Geng, H Tian, Y Yu, S Xu, L Wang, Q Ying, and J Cao. 2019. Landsat time series shows vegetation recovery in ecologically fragile karst regions of southwest China from 1988-2016. Remote Sensing 11(17), 2044

Easterday, K, C Kislik, T E Dawson, S Hogan, and M Kelly. 2019. Remotely sensed water limitation in vegetation: insights from an experiment with unmanned aerial vehicles (UAVs). Remote Sensing 11(16):1853


We used multispectral imagery from quadcopter UAVs to monitor the progression of a water manipulation experiment on a common shrub, Baccharis pilularis (coyote brush) at the Blue Oak Ranch Reserve (BORR) ~20 km east of San Jose, California. We recorded multispectral imagery at several altitudes with nearly hourly intervals to explore the relationship between two common spectral indices, NDVI (normalized difference vegetation index) and NDRE (normalized difference red edge index), leaf water content and water potential as physiological metrics of plant water status, across a gradient of water deficit.

Csillik, O, M Belgiu, G Asner and M Kelly. 2019. Object-Based Time-Constrained Dynamic Time Warping Classification of Crops Using Sentinel-2. Remote Sensing 11(10), 1257


Increasing volume of remote sensing data with improved spatial and temporal resolutions generates unique opportunities for monitoring and mapping of crops. We compared multiple single-band and multi-band object-based time-constrained Dynamic Time Warping (DTW) classifications for crop mapping based on Sentinel-2 time series of vegetation indices.

Palomino, J and M Kelly. Differing sensitivities to fire disturbance result in large differences among remotely-sensed products of vegetation disturbance. Ecosystems


Wondering how different #Landsat products map disturbance? We compare #fire disturbance in #LANDFIRE, Global Forest Change (#GFC) and the North America Forest Dynamics (#NAFD) products in California using #GoogleEarthEngine. This work can help users choose the appropriate product for their needs.

Nikolaeva, S, K O’Hara and M Kelly. 2019. Implications of Forest Stewardship Council Certification for Forest Management in Primorsky Krai in the Russian Far East.  Journal of Sustainable Forestry

Hu, T, Q Ma, Y Su, J J Battles, B M Collins, S Stephens, M Kelly and Q Guo. 2019. A simple and integrated approach for fire severity assessment using bi-temporal airborne LiDAR data. International Journal of Applied Earth Observations and Geoinformation 78: 25-38


We proposed a new LiDAR-based profile area change (PAC) method for fire severity assessment. PAC metrics are highly correlated to field measured changes in basal area and leaf area index. PAC metrics outperformed traditional LiDAR-based canopy cover and tree height change metrics, and Landsat-derived RdNBR.



Csillik, O, J Cherbini, R Johnson, A Lyons, and M Kelly. 2018. Identification of citrus trees from UAV imagery using Convolutional Neural Networks. Drones 2(4), 39

We detected citrus and other crop trees from UAV images using a simple convolutional neural network (CNN) algorithm, followed by a classification refinement using superpixels derived from a Simple Linear Iterative Clustering (SLIC) algorithm. The workflow performed well in a relatively complex agricultural environment with multiple targets, multiple size trees and ages, etc.

Kislik, C, I Dronova, and M Kelly. 2018. UAVs in support of algal bloom research: A review of current applications and future opportunities. Drones 2(4): 35


Unmanned aerial vehicles (UAVs) have recently emerged as another tool for algal bloom detection, providing users with on-demand high spatial and temporal resolution at lower costs. This review explores the current state of this field, and highlights opportunities that could promote its growth.

Easterday, KJ, T Paulson, P DasMohapatra, P Alagona, S Feirer and M Kelly. 2018. From the field to the cloud: A review of three approaches to sharing historical data from field stations using principles from data science.  Frontiers in Environmental Science: 6:(88)


To encourage greater use of historical data across scientific disciplines it is vital to make data findable, accessible, interoperable, and reusable. We discuss the potential of historical dark data to contribute to the modern digital ecological data landscape by focusing on 3 cases from UC field and research stations and the groups that have worked to make historical dark data discoverable. Each case and the methods employed are unique, and showcase varying levels of success in achieving the FAIR principles and shepherding historical data into the 21st century.

Ma, Q, Y Su, L Luo, L Li, M Kelly, and Q Guo. 2018. Evaluating the uncertainty of Landsat-derived vegetation indices in quantifying forest fuel treatments using bi-temporal LiDAR data. Ecological Indicators 95(1): 298-310

Luo, L, Y Su, Q Ma, M Kelly, and Q Guo. 2018. A simple method for direct crown base height estimation of individual trees using airborne LiDAR data. Optics Express


We present a new method for directly estimating individual tree crown base height (CBH) from airborne LiDAR data.

Eisen, RJ, S Feirer, A Monaghan, K Padgett, MB Hahn, and R Lane and M Kelly. 2018. A climate suitability model of the western blacklegged tick (Ixodes pacificus) in California forests, grasslands, scrub-shrublands and riparian areas. Journal of Medical Entomology 55 (5): 1133–1142


We employed an ensemble species distribution modeling approach to identify suitable climatic conditions for Ixodes pacificus (the primary vector of Lyme disease in the western US) and restricted the results to land cover classes where these ticks are typically encountered (forest, grass, scrub-shrub, riparian).

Kelly, M, Y Su, S Di Tommaso, B Collins, D Fry, S L Stephens, and Q Guo. 2018. Impact of error in Lidar-derived canopy height and canopy base height on modeled wildfire behavior in the Sierra Nevada, California, USA. Remote Sensing 10(1): 10 


We evaluated the influence of error associated with two Lidar data products -- canopy height (CH) and canopy base height (CBH) -- on simulated fire behavior.

Easterday, K, P McIntyre and M Kelly. 2018. Exploring the influence of land ownership on 20th century changes to forest structure in California. Forest Ecology and Management 422137–146


Understanding change to forests across land ownership is essential for their management. We compared historical and contemporary forest structural data by ownership class. We found consistent trends statewide, with important differences. Forest densification was largest on private timberlands. Private timberlands and national park/wilderness areas had largest large tree loss.



Kelly, M, K J Easterday, M Koo, J H Thorne, S Mukythar and B Galey. 2017. Geospatial informatics key to recovering and sharing historical ecological data for modern use. Photogrammetric Engineering and Remote Sensing 83(11): 779–786

Boisrame, GF, SS Thompson, M Kelly, S Stephens, and J Cavalli. 2017. Vegetation Change Induced by Changing Fire Regime. Forest Ecology and Management 402: 241–252

Tsalyuk, M, M Kelly, and W Getz. 2017. Improving the measurement of African savanna vegetation using time series analysis of MODIS vegetation indices. ISPRS Journal of Photogrammetry and Remote Sensing 131: 77–91


We analyze time series of four MODIS Vegetation Products (VPs): Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index (EVI), Leaf Area Index (LAI), and Fraction of Photosynthetically Active Radiation (FPAR) for Etosha National Park, a semiarid savanna in north-central Namibia, Africa. We create models to predict the density, cover, and biomass of savanna grass, shrubs, and trees.

Kelly, M 2017. Chapter 6: Mapping Forest Conditions Past, Present, and Future. In Gutiérrez, R J, P N Manley, and P A Stine, technical editors. The California spotted owl: current state of knowledge. Gen. Tech. Rep. PNWGTR-254. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station. 294 p.


Mapping technology has been critical to understanding the ways owls use their forest habitat and to help manage forests for their sustainability. I reviewed papers published from 1992 - 2013 that described the use of remote sensing, aerial imagery, or other mapped products to assess forest structure used by California spotted owls across scales and that also were specific about mapping protocols.

Palomino, J, O Muellerklein, and M Kelly. 2017. A review of the emergent ecosystem of collaborative geospatial tools for addressing environmental challenges. Computers, Environment and Urban Systems 65: 79-92


We develop a typology of the emerging landscape of collaborative geospatial tools (those that use large, multi-scale, multi-temporal, and multi-dimensional spatial data to help collaborators share data, code, and results). Our typology is based on 31 tools, and uses a novel modified K-means clustering algorithm. We identify three primary clusters of tools, driven by required infrastructure and user involvement.

Laraia, B, J Downing,, Y T Zhang, W Dow, M Kelly, S D Blanchard, N Adler, D Schillinger, H H Moffet, M Warton, and A J Karter. 2017. Food environment and weight change: does residential mobility matter? The Diabetes Study of Northern California (DISTANCE). American Journal of Epidemiology 1-8. 

Kelly, M. 2017. Drones in California research and extension. California Agriculture 71(1): 4


Drones are revolutionizing the way we collect data about agricultural and natural resources, and the University of California is poised to be a leader in this emerging field.

Hogan, S D, M Kelly, B Stark, and Y Chen. 2017. Unmanned aerial systems for agriculture and natural resources. California Agriculture 71(1): 5-14

Schile, L M, J C Callaway, K N Suding, and N M Kelly. 2017. Can community structure track sea-level rise? Stress and competitive controls in tidal wetlands. Ecology and Evolution 1(1): 1-10


We simulated sealevel rise across existing and potential marsh elevations in two tidal wetlands differing in salinity. Plants were grown individually and together at five tidal elevations and harvested to assess differences in biomass after one growing season. Increasing inundation reduced biomass of the species commonly found at higher marsh elevations, with little effect on the species found along channel margins.


Kramer, H A, B M Collins, C V Gallagher, J Keane, S L Stephens, and M Kelly. 2016. Accessible LiDAR: estimating large tree density for habitat identification. Ecosphere 7(12): e01593


This study derived a simple and effective method for estimating the density of large-stemmed trees from the LiDAR canopy height model, a standard raster product derived from the LiDAR point cloud that is often delivered with the LiDAR and is easy to process by resource managers trained in geographic information systems (GIS)

Easterday, KJ, P J McIntyre, J Thorne, MJ Santos, and M Kelly. 2016. Assessing threats and conservation status of historical centers of oak richness in California. Urban Planning  1(4): 65–78


We investigated the effects of human urban development on oak species in California by modeling historical patterns of richness for 8 oak tree species using historical map and plot data VTM collection, and then examined spatial intersections between hot spots of historical oak richness and modern urban and conservation lands.

Tamayo, A, M S Mahasin, B A Laraia, E M Warton, S D Blanchard, N M Kelly, H H Moffet, N Adler, D Schillinger, and A J Karter. 2016. Police Recorded Crime and Perceived Stress Among Patients with Type 2 Diabetes: The Diabetes Study of Northern California (DISTANCE). Journal of Urban Health 93(50): 745–757

Kelly, M, K J Easterday, G Rapacciuolo, M S Koo, P Mcintyre, and J Thorne. 2016. Rescuing and sharing historical vegetation data for ecological analysis: The California Vegetation Type Mapping project. Biodiversity Informatics 11: 40-62


Research efforts that synthesize historical and contemporary ecological data with modeling approaches improve our understanding of the complex response of species, communities, and landscapes to changing biophysical conditions through time and in space. Historical ecological data are particularly important in this respect.

Kramer, H A, B M Collins, F K Lake, M K Jakubowski, M Kelly, and S L Stephens 2016. Estimating ladder fuels: a new approach combining field photography with LiDAR. Remote Sensing 8(9), 766

Xiao, P, X Zhang, D Wang, M Yuan, X Feng, M Kelly. 2016. Change detection of built-up land: A framework of combining pixel-based detection and object-based recognition. ISPRS Journal of Photogrammetry and Remote Sensing 119; 402–414


We propose a new framework that combines pixel-level change detection and object-level recognition to detect changes of built-up land from high-spatial resolution remote sensing images.

Su, Y, Q Guo, B M Collins, D Fry, and M Kelly. 2016. Forest fuel treatment detection using multi-temporal airborne Lidar data and high resolution aerial imagery: A case study in the Sierra Nevada, California. International Journal of Remote Sensing 37(14): 3322–3345


Identifying the actual extent of fuel treatments in forests is of primary importance to understand their influence. Lidar is a powerful remote sensing tool that can provide accurate measurements of forest structures and has great potential for monitoring forest changes. We use canopy height model and canopy cover products derived from multi-temporal Lidar data to monitor forest changes following the implementation of landscape-scale fuel treatments.

Müller, M F, S E Thompson, and M Kelly. 2016. Bridging the information gap: A webGIS tool for rural electrification in data-scarce regions. Applied Energy 171(1): 277-286


We present a method to site, size and evaluate the potential for micro hydropower based on remote sensing data.

Su, Y, Q Guo, DL Fry, BM Collins, M Kelly, JP Flanagan, and JJ Battles. 2016. A vegetation mapping strategy for conifer forests by combining airborne lidar data and aerial imagery. Canadian Journal of Remote Sensing 42:1–15 


We introduce a strategy using both multispectral aerial imagery and Lidar data to map vegetation composition and structure over large spatial scales.

Eitzel, M V, M Kelly, I Dronova, J Solera, and P de Valpine. 2016. Challenges and opportunities in synthesizing historical geospatial data using statistical models. Ecological Informatics 31 (2016): 100-111


We classified land cover types from 1940s historical aerial imagery using Object Based Image Analysis (OBIA) and compared these maps with data on recent cover.


Tempel, D. J., R. J. Gutiérrez, J. J. Battles, D. L. Fry, Y. Su, Q. Guo, M. J. Reetz, S. A. Whitmore, G. M. Jones, B. M. Collins, S. L. Stephens, M. Kelly, W. J. Berigan, and M. Z. Peery. 2015. Modeling short- and long-term impacts of fuel treatments and wildfire on an old-forest species. Ecosphere 6(12): Article 261


Fuels-reduction treatments are commonly implemented in the western US to reduce the risk of high-severity fire, but they may have negative short-term impacts on species associated with older forests. We modeled the effects of a completed fuels-reduction project on fire behavior and California spotted owl (Strix occidentalis occidentalis) habitat and demography in the Sierra Nevada to assess the potential short- and long-term trade-offs.

O’Connnell, J., K. Byrd, and M. Kelly. 2015. A hybrid modeling approach for mapping relative differences in belowground biomass and root:shoot ratios using spectral reflectance, foliar N and plant biophysical data. Remote Sensing 7, 16480-16503


We used remotely-sensed estimates of two aboveground plant characteristics, aboveground biomass and % foliar N to explore biomass allocation in low diversity freshwater impounded peatlands (Sacramento-San Joaquin River Delta, CA, USA).

Turpie, K, V V Klemas, K Byrd, M Kelly, J Heon-Young. 2015. Prospective HyspIRI global observations of tidal wetlands. Remote Sensing of Environment 16: 206-217


This paper describes how the HyspIRI hyperspectral and thermal infrared sensors can be used to study and map key ecological properties, such as species composition, biomass, hydrology, and evapotranspiration of tidal salt and brackish marshes and mangroves, and perhaps other major wetland types, including freshwater marshes and wooded/shrub wetlands.

Lei, S. and M. Kelly. 2015. Evaluating adaptive collaborative management in Sierra Nevada forests by exploring public meeting dialogues using Self-Organizing Maps. Society and Natural Resources (28)8: 873-890 


Self-organizing maps (SOM), an unsupervised machine-learning method, were used to process, organize, and visualize public meeting notes from a decade of public meetings as part of the Sierra Nevada Adaptive Management Project (SNAMP).

Kelly, M. and S. Di Tommaso. 2015. Mapping forests with Lidar provides flexible, accurate data with many uses. California Agriculture 69(1): 14-20


The use of remote sensing for forest inventory, fire management, and wildlife habitat conservation planning has a decades-long and productive history, especially in California. This paper reviews this use, and highlights Lidar remote sensing.

Lei, S., A. Iles, and M. Kelly. 2015. Characterizing the networks of digital information that support collaborative adaptive forest management in Sierra Nevada forests. Environmental Management 56(1): 94-109


We use powerful new information monitoring tools to characterize information products generated in the SNAMP program through their production, transport, use, and monitoring.

Zhang, Y.T., B.A. Laraia, M.S. Mujahid, A. Tamayo, S.D. Blanchard, E.M. Warton, M. Kelly, H.H. Moffet, D. Schillinger, N. Adler, and A.J. Karter. 2015. Does food vendor density mediate the association between neighborhood deprivation and BMI?: A G-computation mediation analysis. Epidemiology 26(3): 344-52


We assessed whether the association between neighborhood deprivation and BMI is attributable, in part, to geographic variation in the availability of healthful and unhealthful food vendors.

Tsalyuk, M., M. Kelly, K. Koy, Wayne M. Getz, and H. S. Butterfield. 2015. Monitoring the Impact of Grazing on Rangeland Conservation Easements Using MODIS Vegetation Indices. Journal of Rangeland Management 68(2): 173–185


Residual dry matter (RDM), the dry grass biomass left on the ground in the fall, is a widely used proxy for rangeland conditions. We developed a method to efficiently monitor RDM using time series of three Moderate Resolution Imaging Spectroradiometer (MODIS) satellite-based vegetation indices (VIs).

Li, L., Q. Guo, S. Tao, M. Kelly, and G. Xu. 2015. Lidar with multi-temporal MODIS provide a means to upscale predictions of forest biomass. ISPRS Journal of Photogrammetry and Remote Sensing 102: 198–208


We use airborne Lidar to bridge the scale gap between satellite-based and field-based studies, and evaluate satellite-derived indices to estimate regional forest aboveground biomass.

Butsic, V., M. Kelly, M. Moritz. 2015. Land use and wildfire: a review of local interactions and teleconnections. Land 4(1): 140-156


We review the nuanced land use teleconnections between wildfire and land use.

McIntyre, P.J., J.H. Thorne, C.R. Dolanc, A.L. Flint, L.E. Flint, M. Kelly, and D.D. Ackerly.  2015. 20th century shifts in forest structure in California: denser forests, smaller trees, and increased dominance of oaks. Proceedings of the National Academy of Sciences 112(5): 1458-1463


We document changes in forest structure between historical (1930s) and contemporary (2000s) surveys of California vegetation through comparisons of tree abundance and size across the state and within several ecoregions. Across California, tree density in forested regions increased by 30% between the two time periods, whereas forest biomass in the same regions declined, as indicated by a 19% reduction in basal area.

Lewis, S., S. Gross, A. Visel, M. Kelly, and W. Morrow. 2015. Fuzzy GIS-based multi-criteria evaluation for U.S. Agave production as a bioenergy feedstock. Global Change Biology Bioenergy 7: 84–99 doi: 10.1111/gcbb.12116


In the US renewable energy mandates calling for increased production of cellulosic biofuels will require a diversity of bioenergy feedstocks to meet growing demands, and plants within the genus Agave promise to be a productive feedstock in hot and arid regions. The potential distributions of Agave tequilana and Agave deserti in the United States were evaluated based on plant growth parameters identified in an extensive literature review.



Kelly, A.B, and M. Kelly. 2014. Validating the remotely sensed geography of crime: A review of emerging issues. Remote Sensing 6(12): 12723-12751


We explore the existing literature (61 papers as of Dec 2014) on the active detection of crimes using remote sensing technologies, and ask critical questions about efficacy, technology and implications.

Laraia, B.A., S.D. Blanchard, A.J. Karter, J.C. Jones-Smith, E.M. Warton, E. Kersten, M. Jerrett, H.H. Moffett, N. Adler, D. Schillinger and M. Kelly. 2014. Spatial pattern of Body Mass Index among adults in the Diabetes Study of Northern California (DISTANCE). International Journal of Health Geographics 13:48


We evaluated the extent to which spatial clustering of extreme body mass index (BMI) values among a large sample of adults with diabetes was explained by individual characteristics and contextual factors.

Ferranto, S., L. Huntsinger and M. Kelly. 2014. Sustaining ecosystem services from private lands in California: the role of the landowner. Rangelands 36(5): 44-51


Landowner participation in sustaining ecosystem services means conservation initiatives need to build on landowner management objectives, practices, and goals, and encourage collaboration across multiple parcels.

Tao, S., Li, L., Q. Guo, L. Li, B. Xue, M. Kelly, W. Li, G. Xu, and Y. Su. 2014. Airborne Lidar-derived volume metrics for aboveground biomass estimation: A comparative assessment for conifer stands. Agriculture and Forest Management 198–199 (2014) 24–32


We compared a range of airborne Lidar-derived volume metrics (i.e. stem volume, crown volume under convex hull, and crown volume under Canopy Height Model (CHM)) to estimate aboveground biomass.

Kramer, H. A., B. Collins, M. Kelly, S. Stephens. 2014. Quantifying ladder fuels in forests: a new approach using LiDAR. Forests 5:1432-1453


We investigated the relationship between LiDAR and ladder fuels in the northern Sierra Nevada, California USA.

Byrd, K., J. O’Connell, S. Di Tomasso, and M. Kelly. 2014. Evaluation of sensor types and environmental controls on mapping biomass of coastal marsh emergent vegetation. Remote Sensing of Environment 149:166-180


We modeled biomass of emergent vegetation with field spectrometer and satellite data from Landsat, Hyperion and WorldView-2 sensors.

O’Connell, J. L., K. B. Byrd, and M. Kelly. 2014. Remotely-sensed indicators of N-related biomass allocation in Schoenoplectus acutus. PLOS One 9(3): e90870


We used N-addition and control plots (4 each) to test whether remotely-sensed vegetation indices could predict leaf N concentration, root:shoot ratios and belowground biomass of SSchoenoplectus acutus.

Lewis, S. and M. Kelly. 2014. Mapping the potential for biofuel production on marginal lands: differences in definitions, data and models across scales. ISPRS International Journal of Geo-Information 3(2), 430-459


We reviewed a collection of recent literature that mapped bioenergy potential on marginal lands at varying scales, and found that there is no common working definition of marginal land across all of these works. Specifically we found considerable differences in mapped results that are driven by dissimilarities in definitions, model framework, data inputs, scale and treatment of uncertainty.

Lewis, S. M., G. Fitts, M. Kelly, and L. Dale. 2014. A fuzzy logic-based spatial suitability model for drought-tolerant switchgrass in the United States. Computers and Electronics in Agriculture 103: 39-47


This paper outlines a spatial suitability modeling approach to map potential for switchgrass that incorporates fuzzy logic and utilizes both physical and economic variables.

Schile, L. M., J. C. Callaway, J. T. Morris, D. Stalberg, V. T. Parker, and M. Kelly. 2014. Modeling tidal marsh distribution with sea-level rise: evaluating the role of vegetation, sediment, and upland habitat in marsh resiliency. PLOS One 9(2): e88760


We examined marsh resiliency under these uncertainties using the Marsh Equilibrium Model, a mechanistic, elevation-based soil cohort model, using a rich data set of plant productivity and physical properties from sites across the estuarine salinity gradient.

Blaschke, T., G. J. Hay, M. Kelly, S. Lang, P. Hofmann, E. Addink, R. Queiroz Feitosa, F. van der Meer, H. van der Werff, F. van Coillie, and D. Tiede. 2014. Geographic Object Based Image Analysis: a Paradigm in Remote Sensing and Geographic Information Science? ISPRS Journal of Photogrammetry and Remote Sensing 87(1), 180-191


We investigate development in OBIA and ask whether or not this is a new paradigm in remote sensing and Geographic Information Science (GIScience).


Peña-Barragan, J. M., J. Torres-Sánchez, A. I. de Castro, M. Kelly, and F. López-Granados. 2013. Generating weed maps in early-season maize fields by using an unmanned aerial vehicle (UAV) and object-based image analysis. PLOS One 8(10): e77151


A robust and entirely automatic object-based image analysis (OBIA) procedure was developed on a series of UAV images using a six-band multispectral camera (visible and near-infrared range) with the ultimate objective of generating a weed map in an experimental maize field in Spain.

Pennypacker, C.R., M.K. Jakubowski, M. Kelly, M. Lampton, C. Schmidt, S. Stephens, and R. Tripp. 2013. FUEGO—Fire Urgency Estimator in Geosynchronous Orbit—A proposed early-warning fire detection system. Remote Sensing 5(10): 5173-5192


We propose the framework for a geosynchronous satellite with modern imaging detectors, software, and algorithms able to detect heat from early and small fires, and yield minute-scale detection times.

Ferranto, S., L. Huntsinger, C. Getz, W. Stewart, G. Nakamura, and M. Kelly. 2013. Management without borders? A survey of landowner practices and attitudes towards cross- boundary cooperation. Society and Natural Resources 26(9): 1082-1100


Results from a landowner survey in California were analyzed using an audience segmentation approach. Landowners were grouped into four clusters according to ownership motivations: rural lifestyle, working landscape, natural amenity, and financial investment.

Jakubowski, M. J., W. Li, Q. Guo, and M. Kelly. 2013. Delineating individual trees from lidar data: a comparison of vector- and raster-based segmentation approaches. Remote Sensing, 5: 4163-4186


This work concentrates on delineating individual trees from discrete lidar data in topographically-complex, mixed conifer forest across the California’s Sierra Nevada. We delineated individual trees using vector data and a 3D lidar point cloud segmentation algorithm, and using raster data with an object-based image analysis (OBIA) of a canopy height model (CHM).

Jones-Smith, J. C., M. Wharton, M. Kelly, E. Kersten, A. Karter, N. Adler, D. Schillinger, H. Moffett, and B. A. Laraia. 2013. Obesity and the food environment: income and ethnicity differences among people with diabetes, the Diabetes Study of Northern California (DISTANCE). Diabetes Care 36: 2697-2705

Schile, L. K. Byrd, L. Windham-Meyers, and M. Kelly. 2013. Accounting for plant litter in remote sensing based estimates of carbon flux in wetlands. Remote Sensing Letters 4:6, 542-551


We tested agricultural- and forest-based methods for estimating the fraction of absorbed photosynthetically active radiation (ƒAPAR), a key parameter for modeling gross primary productivity (GPP), in a restored, managed wetland with a dense litter layer of non-photosynthetic vegetation, and we compared the difference in canopy light transmission between a tidally influenced wetland and the managed wetland.

Jakubowski, M. Q. Guo, B. Collins, S. Stephens, and M. Kelly. 2013. Prediction of fuel models and stand structure metrics using lidar and optical remote sensing in dense mixed conifer forest. Photogrammetric Engineering and Remote Sensing 79(1): 37-50 (ASPRS Award*)


We compared the ability of several classification and regression algorithms to predict forest stand structure metrics and standard surface fuel models.

Brown, G., M. Kelly and D. Whital. 2013. Which “public”? Sampling effects in public participation GIS (PPGIS) and Volunteered Geographic Information (VGI) systems for public lands management. Journal of Environmental Planning and Environment 57(2): 190- 214. doi:


We examined the effects of sampling in a PPGIS/VGI application for national forest planning in the U.S. The volunteer public group expressed stronger utilitarian values and consumptive use preferences while the random sample group preferred forest amenities.

Jakubowski, M. K., Q. Guo, and M. Kelly. 2013. Tradeoffs between lidar pulse density and forest measurement accuracy. Remote Sensing of Environment 130: 245-253


In this study, we systematically investigated the relationship between pulse density and the ability to predict several commonly used forest measures and metrics at the plot scale. The accuracy of predicted metrics was largely invariant to changes in pulse density at moderate to high densities.


Connors, J., S. Lei, and M. Kelly. 2012. Citizen science in the age of neogeography: utilizing volunteered geographic information for environmental monitoring.  Annals of the Association of American Geographers 102(6):1267-1289

Zhao, F., Q. Guo, and M. Kelly. 2012. Allometric equation choice impacts lidar-based forest biomass estimates: A case study from the Sierra National Forest, CA. Agriculture and Forest Meteorology 165: 64-72

Kersten, E., B. Laraia, M. Kelly, K. Adler, and I. Yen. 2012. Do small food stores provide access to nutritious foods? Comparing database and store visit measures of the community nutrition environment. Preventing Chronic Disease, 9:120023. DOI:

Plieninger, T., S. Ferranto, L. Huntsinger, M. Kelly, and C. Getz. 2012. Appreciation, use, and management of biodiversity and ecosystem services in California’s working landscapes. Environmental Management. DOI: 10.1007/s00267-012-9900-z

Zhao, F., A. R. Sweitzer, Q. Guo and M. Kelly. 2012. Characterization of forest habitat for mammals with lidar: a case study of Pacific fisher denning trees in the Sierra National Forest, CA. Forest Ecology and Management 280: 112–119

Kelly, M., S. Ferranto, K. Ueda, S. Lei and L. Huntsinger. 2012. Expanding the table: the web as a tool for participatory adaptive management in California forests. Journal of Environmental Management 109:1-11

Baldocchi, D., M. Detto, O. Sonnentag, Verfaillie, Y. Teh, W. Silver, and M. Kelly. 2012. The challenges of measuring methane fluxes and concentrations over a peatland pasture. Agricultural and Forest Meteorology 153(1): 177-187

Ferranto, S., L. Huntsinger, C. Getz, W. Stewart, G. Nakamura, and M. Kelly. 2012. Consider the source: The impact of media and authority in outreach to California’s forest and rangeland owners. Journal of Environmental Management 97(1): 131-140

Li, W., Q. Guo, M. Jakubowski and M. Kelly. 2012. A new method for segmenting individual trees from the lidar point cloud. Photogrammetric Engineering and Remote Sensing 78(1): 75-84


García-Feced, C., D. Temple, and M. Kelly. 2011. LiDAR as a tool to characterize wildlife habitat: California Spotted Owl nesting habitat as an example. Journal of Forestry 108(8): 436-443

Blanchard, S., M. Jakubowski, and M. Kelly. 2011. Object-based image analysis of downed logs in a disturbed forest landscape using lidar. Remote Sensing 3(11), 2420-2439

Stralberg, D., M. Brennan, J. C. Callaway, J. K. Wood, L. M. Schile, D. Jongsomjit, M. Kelly, V. T. Parker, and S. Crooks. 2011. Evaluating tidal marsh sustainability in the face of sea-level rise: a hybrid modeling approach applied to San Francisco Bay. PLOS One 6(11): e27388


We developed a hybrid approach that involves a mechanistic treatment of marsh accretion dynamics and incorporates spatial variation at a scale relevant for conservation and restoration decision-making. We applied this model to San Francisco Bay, using best-available elevation data and estimates of sediment supply and organic matter accumulation developed for 15 Bay subregions.

Kelly M., S. Blanchard. E. Kersten, and K. Koy. 2011. Terrestrial remotely sensed imagery in support of public health: New avenues of research using object-based image analysis. Remote Sensing 3(11): 2321-2345

Ferranto, S., L. Huntsinger, C. Getz, G. Nakamura, W. Stewart, S. Drill, Y. Valacovich, M. DeLasaux, and M. Kelly. 2011. Forest and rangeland owners value land for natural amenities and as financial investment. California Agriculture 65(4): 184-191

Sonnentag O., R. Vargas, M. Detto, B. R. K. Runkle, Y. A. Teh, W. L. Silver, M. Kelly, and D. D. Baldocchi. 2011. Tracking the structural and functional development of a perennial pepperweed (Lepidium latifolium L.) infestation using a multi-year archive of webcam imagery and eddy covariance measurements. Agricultural Forest Meteorology 151:916-926

Leung, C.H., B.A. Laraia, M. Kelly, D. Nickleach, N.E. Adler, L.H. Kushi, and I.H. Yen. 2011. The influence of neighborhood food stores on change in young girls’ body mass index. American Journal of Preventative Medicine 41(1): 43–51

Koy, K., S. V. Wart, B. Galey, M. O’Connor, and M. Kelly. 2011. Cal-Adapt: Bringing global climate change data to local application. Photogrammetric Engineering and Remote Sensing 77(6): 546-550

Teh, Y. A., W. L. Silver, O. Sonnentag, M. Detto, M. Kelly, and D. D. Baldocchi. 2011. Large greenhouse gas emissions from a temperate peatland pasture. Ecosystems 14: 311–325

Sonnentag, O., M. Detto, B.R.K. Runkle, M. Kelly, and D.D. Baldocchi. 2011. Carbon dioxide exchange of a pepperweed (Lepidium latifolium L.) infestation: how do flowering and mowing affect canopy photosynthesis and autotrophic respiration? Journal of Geophysical Research – Biogeosciences, 116, G01021, doi:10.1029/2010JG001522

Tuxen, K., L. Schile, D. Stralberg, S. Siegel, V. T. Parker, M. Vasey, J. Callaway and M. Kelly. 2011. Mapping changes in tidal wetland vegetation composition and pattern across a salinity gradient using high spatial resolution imagery. Wetlands Ecology and Management 19:141-157

Kelly, M., Tuxen, K., and D. Stralberg. 2011. Mapping changes to vegetation pattern in a restoring wetland: finding pattern metrics that are consistent across scale and time. Ecological Indicators 11: 263-273


McPherson, B. M., D. L. Wood, S. Mori, M. Kelly, A. J. Storer, P. Svihra, and R. B. Standiford. 2010. Responses of oaks and tanoaks to the sudden oak death pathogen after 8 y of monitoring in two coastal California forests. Forest Ecology and Management 259: 2248-2255

De Chant, T., A. H. Gallego, J. V. Saornil and M. Kelly. 2010. Urban influence on changes in linear forest edge structure. Landscape and Urban Planning 96: 12-18

Stralberg, D., M. Herzog, N. Nur, K. Tuxen, S. Siegel and M. Kelly. 2010. Predicting avian abundance within and across tidal marshes using fine-scale vegetation and geomorphic metrics. Wetlands 30: 475-487


De Chant, T. and M. Kelly. 2009. Individual object change detection for monitoring the impact of a forest pathogen on a hardwood forest.  Photogrammetric Engineering and Remote Sensing 75(8): 1005-1013

Zeledon, E. and M. Kelly. 2009. Understanding large-scale deforestation in southern Jinotega, Nicaragua from 1978 to 1999 through the examination of changes in land use and land cover. Journal of Environmental Management 90: 2866-2872

Collins, B., J. Miller, M. Kelly, J.W. van Wagtendonk, and S. L. Stephens.  2009. Interactions among wildland fires in a long-established Sierra Nevada natural fire area. Ecosystems 12(1): 114-128


Kelly, M., D. Liu, B. McPherson, D. Wood and R. Standiford. 2008. Spatial pattern dynamics of oak mortality and associated disease symptoms in a California hardwood forest affected by sudden oak death. Journal of Forest Research 13:312-319

Kelly, M., K. Ueda and B. Allen-Diaz. 2008. Considerations for ecological reconstruction of historic vegetation: Analysis of the spatial uncertainties in the California Vegetation Type Map dataset. Plant Ecology 194 (1): 37-49

Cleve, C., M. Kelly F. Kearns and M. Moritz. 2008. Classification of urban environments for fire management support: A comparison of pixel- and object-based classifications using high-resolution aerial photography. Computers, Environment and Urban Systems 32: 317–326

Rindfuss, R. R, B. Entwisle, S. J. Walsh, L. An, N. Badenoch, D.G. Brown, P. Deadman, T. P. Evans, J. Fox, J. Geoghegan, M. Gutmann, M. Kelly, M. Linderman, J. Liu, G. P. Malanson, C. F. Mena, J. P. Messina, E. F. Moran, D. C. Parker, W. Parton, P. Prasartkul, D. Robinson, Y. Sawangdee, L. K. VanWey, P. H. Verburg, and G. Zhong. 2008. Land use change: complexities and comparisons. Journal of Land Use Science 3(1): 1-10

Liu, Y., Q. Guo, and M. Kelly.  2008. A framework of region-based spatial relationships for non-overlapping features and its application in object based image analysis.  ISPRS Journal of Photogrammetry and Remote Sensing 63: 461–475

Tuxen, K., L. Schile, M. Kelly, and S. Siegel. 2008. Vegetation colonization in a restoring tidal marsh: A remote sensing approach. Restoration Ecology 16(2): 313-323

Pu, R., M. Kelly, G. L. Anderson and P. Gong. 2008. Spectroscopic determination of health levels of coast live oak (Quercus agrifolia) leaves. GeoCarto International 23 (1): 3-20

Pu, R., M. Kelly, G. L. Anderson, and P. Gong. 2008. Using CASI hyperspectral imagery to detect mortality and vegetation stress associated with a new hardwood forest disease. Photogrammetric Engineering & Remote Sensing 74(1): 65-75

Lozano, F. J, S. Suárez-Seoane, M. Kelly, and E. Luis. 2008. Multi-scale approach to fire occurrence probability in a Mediterranean region using satellite data and CART. Remote Sensing of Environment 112(3): 708-719


Liu, D., M. Kelly, P. Gong and Q. Guo. 2007. Characterizing spatial-temporal tree mortality patterns associated with a new forest disease. Forest Ecology and Management 253 (1-3): 220-231

Kelly, M., Q. Guo, D. Liu and D. Shaari. 2007. Modeling the risk of a new invasive forest disease in the United States: an evaluation of five environmental niche models. Computers, Environment and Urban Systems 31(6): 689-710

Pederson, B., F. Kearns and M. Kelly. 2007. Methods for facilitating web-based participatory research informatics. Ecological Informatics 2(1): 33-42

Collins, B. M., M. Kelly, J. W. V. Wagendonk and S. L. Stephens. 2007. Spatial patterns of large natural fires in Sierra Nevada wilderness areas. Landscape Ecology 22(4): 545-557

Guo, Q. C., M. Kelly, P. Gong and D. Liu.  2007. An object-based classification approach in mapping tree mortality using high spatial resolution imagery. GIScience and Remote Sensing 44(1):  24–47

Byrd, K., M. Kelly and A. Merenlender. 2007. Temporal relationships between watershed land use and salt marsh disturbance in a Pacific estuary. Environmental Management 39(1): 98-112


Byrd, K. and M. Kelly. 2006. Salt marsh vegetation response to edaphic and topographical changes from upland sedimentation in a Pacific estuary.  Wetlands 26(3): 813-829

Liu, D., P. Gong, Q. Guo, and M. Kelly. 2006. Automatic registration of airborne images by combining area-based methods with local transformation methods. Photogrammetric Engineering and Remote Sensing 72(9): 1049-1059

Chen, Q., D. Baldocchi, P. Gong, and M. Kelly. 2006. Isolating individual trees in a savanna woodland using small footprint LIDAR data. Photogrammetric Engineering and Remote Sensing 72(8): 923-932

Fisher, J., M. Kelly and J. Romm. 2006. Scales of environmental justice: combining GIS and spatial analysis for air toxics in West Oakland, California. Health and Place 12: 701-714

Yu, Q., P. Gong, N. Clinton, M. Kelly and D. Schirokauer. 2006. Object-based detailed vegetation classification with airborne high resolution remote sensing imagery.  Photogrammetric Engineering and Remote Sensing 72(7): 799-811

Liu, D., M. Kelly, and P. Gong. 2006. A Spatial-temporal approach for monitoring forest disease dynamics using multi-temporal high spatial resolution imagery.  Remote Sensing of Environment 101(2): 167-180


Opperman, J. J., K. Lohse, C. Brooks, N. M. Kelly and A. M. Merenlender. 2005. Influence of watershed-scale land use on salmonid spawning habitat in a Mediterranean-climate basin, California. Canadian Journal of Fisheries and Aquatic Science 62: 2740-2751

Kelly, M., B. Allen-Diaz, and N. Kobzina. 2005. Digitization of a historic dataset: the Wieslander California vegetation type mapping project. Madroño 52(3):191-201

Sun, W, M. Kelly, and P. Gong. 2005. Separation of dead tree crowns from the oak woodland forest mosaic by integrating spatial information. GeoCarto International 20(2): 15-20

McPherson, B. A. D. L. Wood, P. Švihra, A. J. Storer, N. M. Kelly and R. B. Standiford. 2005. Sudden oak death in California: Disease progression in oaks and tanoaks. Forest Ecology and Management 213(1-3): 71-89

Kearns, F. R., N. M. Kelly, J. L. Carter, and V. Resh. 2005. A method for the use of landscape metrics in freshwater research and management. Landscape Ecology 20(1): 113-125

Guo, Q., M. Kelly, and C. Graham. 2005. Support vector machines for predicting distribution of Sudden Oak Death in California. Ecological Modeling 182(1): 75-90 


Byrd, K. B., M. Kelly, and E. Van Dyke. 2004. Decadal changes in a Pacific estuary: a multi-source remote sensing approach for historical ecology. GIScience and Remote Sensing 41(4): 347-370

Kelly, M., D. Shaari, Q. Guo, and D. Liu. 2004. A comparison of standard and hybrid classifier methods for mapping hardwood mortality in areas affected by sudden oak death.  Photogrammetric Engineering and Remote Sensing 70(11): 1229-1239

Guo, Q. C., and M. Kelly. 2004. Interpretation of scale in paired quadrat variance methods. Journal of Vegetation Science 15: 763-770

Švihra, P. and M. Kelly. 2004. Importance of oak ambrosia beetles in predisposing coast live oak trees to wood decay. Journal of Aboriculture 30(6): 371-375

Wacker, M. and N. M. Kelly. 2004. Changes in vernal pool edaphic settings through mitigation at the project and landscape scale. Wetlands Ecology and Management 12(3): 165-178

Kelly, M., K. A. Tuxen, and F. R. Kearns. 2004. Geospatial informatics for management of a new forest disease: Sudden Oak Death. Photogrammetric Engineering and Remote Sensing 70(9): 1001-1004

Wacker, M. and N. M. Kelly. 2004. Ranchers vs. ranchettes in California’s oak rangelands. Rangelands 26(1): 17-22

Kelly, M. and D. Liu. 2004. Mapping diseased oak trees using ADAR imagery. Geocarto International 19(1): 57-64


Kearns, F. R., M. Kelly, and K. A. Tuxen. 2003. Everything happens somewhere: using webGIS as a tool for sustainable natural resource management. Frontiers in Ecology and the Environment 1(10): 541-548

Kelly, N. M., and K. Tuxen. 2003. WebGIS for monitoring “sudden oak death” in coastal California. Computers, Environment and Urban Systems 27(5): 527-547

Pu, R., S. Ge, N. M. Kelly, and P. Gong. 2003. Spectral absorption features as indicators of water status in coast live oak (Quercus agrifolia) leaves. International Journal of Remote Sensing 24(9): 1799-1810


Kelly, M., and R. Meentemeyer. 2002. Landscape dynamics of the spread of Sudden Oak Death. Photogrammetric Engineering and Remote Sensing 68(10): 1001-1009

Fonseca, M. S., P. E. Whitfield, N. M. Kelly, and S. S. Bell. 2002. Statistical modeling of seagrass landscape pattern and associated ecological attributes in relation to hydrodynamic setting. Ecological Applications 12(1): 218-237


McPherson, B. A., D. L. Wood, A. J. Storer, N. M. Kelly, and R. B. Standiford. 2001. Sudden oak death, a new forest disease in California. Integrated Pest Management Reviews (3-4): 243-246

Kelly, N. M., and B. A. McPherson. 2001. Multi-scale approach taken to Sudden Oak Death monitoring. California Agriculture. January-February: 15-16

Helly, J. H., N. M. Kelly, D. Sutton, and T. Elvins. 2001. Collaborative management of natural resources in San Diego Bay. Coastal Management 29(2): 117- 132

Kelly, N. M., M. Fonseca, and P. Whitfield. 2001. Predictive mapping for management and conservation of seagrass beds in North Carolina. Aquatic Conservation: Marine and Freshwater Ecosystems 11(6): 437-451

Kelly, N. M. 2001. Changes to landscape pattern of coastal North Carolina wetlands under the Clean Water Act. Landscape Ecology 16(1): 3-16 


Kelly, N. M. 2000. Spatial accuracy assessment of wetland permits. Cartography and Geographic Information Systems 27(2): 117-128