MiCO: Migratory Connectivity in the Ocean Twitter

MiCO System Help

Explore the MiCO System

Browse and see summaries for species / jurisdictional areas / contributors
Directly go to map of species use areas / nodes / metasites / corridors
https://mico.eco/system https://mico.eco/system/mapper
Select species and click “Globe” icon or map image. Select taxon group first, then species.

Suggested citation for MiCO:Dunn, D. C., A.-L. Harrison, C. Curtice, S. DeLand, B. Donnelly, E. Fujioka, E. Heywood, C. Y. Kot, S. Poulin, M. Whitten, S. Åkesson, A. Alberini, W. Appeltans, J. M. Arcos, H. Bailey, L. T. Ballance, B. Block, H. Blondin, A. M. Boustany, J. Brenner, P. Catry, D. Cejudo, J. Cleary, P. Corkeron, D. P. Costa, M. Coyne, G. O. Crespo, T. E. Davies, M. P. Dias, F. Douvere, F. Ferretti, A. Formia, D. Freestone, A. S. Friedlaender, H. Frisch-Nwakanma, C. B. Froján, K. M. Gjerde, L. Glowka, B. J. Godley, J. Gonzalez-Solis, J. P. Granadeiro, V. Gunn, Y. Hashimoto, L. M. Hawkes, G. C. Hays, C. Hazin, J. Jimenez, D. E. Johnson, P. Luschi, S. M. Maxwell, C. McClellan, M. Modest, G. Notarbartolo di Sciara, A. H. Palacio, D. M. Palacios, A. Pauly, M. Rayner, A. F. Rees, E. R. Salazar, D. Secor, A. M. M. Sequeira, M. Spalding, F. Spina, S. Van Parijs, B. Wallace, N. Varo-Cruz, M. Virtue, H. Weimerskirch, L. Wilson, B. Woodward, and P. N. Halpin. 2019. The importance of migratory connectivity for global ocean policy. Proceedings of the Royal Society B: Biological Sciences 286:20191472.

Migratory Connectivity in the Ocean (MiCO). Highly migratory marine species nodes and corridors, developed with data contributed to MiCO. Available from the MiCO System Version 1.0. MiCO. https://mico.eco. Accessed MM/DD/YYYY.

Table of Contents Menu Options on the Mapper

Home: Brings you to the homepage of the MiCO website

Methods: Link to page describing the methods used to generate MiCO products

Online help: Access to this page describing the MiCO user interface

Terms of Use: Link to the MiCO Terms of Use webpage

Taxon Groups: The MiCO species are grouped into “Fish”, “Marine mammals”, “Seabirds” and “Sea turtles”. Each group link brings you to the species list of the group. Select one of the species to explore more. Hold down the control (Windows) or command (Mac) key to select multiple species.

Basics of Map

When you select a species from the main menu, the metasites and corridors of the species are drawn on the map. The legend at the top of the map shows the species name and a list of layers available to the species. If the species does not have metasites or corridors but does have use areas, the use areas will be shown on the map. If the species has use areas, you can turn them on by clicking “ON” in the legend. You can also hide the metasites and/or corridors by clicking “OFF” in the legend.

“Other Layers” in the legend can be clicked to show a list of supplemental layers, which you can turn on and off. The reference layer refers to the distribution map of the species.

The metasites are stored as point locations with a size of the metasite measured as a radius in the MiCO database. A metasite is visualized on the map as a circle with the radius. The inside of the circle is a pie chart comprising the pies of the activities observed in the aggregated sites. The label of a matesite tells you the number of sites aggregated.

The corridors connecting metasites are drawn as curvy lines. The red line represents the going forward move and the blue line is the return to the origin. The width of the lines indicates the number of animals traveling. These lines do not represent the actual paths that the animals travel through.

When you move your mouse over one of the metasites (circle/pie chart), the details of the metasite, including a list of aggregated sites, corridors to and from the metasite and a list of references, will be shown in a popup window. A click on a metasite sets a focus on the metasite and hides other metasites that are far away from the clicked metasites. Overlapping metasites are shifted so that they can be seen without overlaps. Also, the sites aggregated to the metasite (child sites) are visualized with a small, fixed-sized circles. By clicking the same metasite again, the focus is cut off and the map goes back to the previous view.

A similar popup shows up when you mouse over a Use Area polygon. When you click a Use Area polygon, it displays the detailed information of the Use Area.

A mouseover and click event on a corridor works in a similar way. When a corridor is clicked, the source and destination metasites are shown while the other metasites are hidden. A second click on the same corridor gets back to the original view.

Mouse over Click
Metasite
Use Area
Corridor

Map Tools Toolbar

The Map Tools Toolbar will appear when a button below the MiCO logo is clicked.

Zoom Click on one of these icons to use the mouse to draw a box around an area to zoom in to or out of.
Reset Map Extent Click on this icon to return the map to the initial extent view.
Select Region of Interest Click on the box icon to draw a rectangular region on the map; click on the polygon icon to draw a polygon region, clicking for each vertex. Once a region has been created, use the red “X” to remove it by clicking on the red “X” and then clicking on the region to be removed. Clicking within the polygon that is created will bring up a popup window that shows the data that intersects with the region of interest.
Split Screen Maps Clicking on this icon either splits the screen into two maps or returns a split screen back to one single map screen. Clicking the drop-down menu gives the user the options to synchronize the two maps (when panning or zooming) or to overlap the two maps. When the two maps are synchronized, a little note will appear under the tab menu items: “Two maps sync’ed.” When the “overlap two maps” option is selected, a vertical movable bar will appear on the screen. As you slide the bar to the left or right, the results selected in each map will appear on the appropriate side of the slider.
Full screen mode This mode also hides the main menu panel along the right side of the map. “ESC” to return to regular view.

Main Menu & Features

Once you selected the species, the main menu & features are displayed as auto-shrink tool buttons. Each button brings up the associated panel. Each feature is described in details in the following sections.

Species Go back to the species list panel with four taxon groups as the header. The icon changes according to the taxon group chosen.
Filtering The “Filtering” panel allows you to refine the results based on one or more criteria including activities and individual use areas / metasites.
Results Information about the selected and filtered products. Summary stats and several interactive charts are displayed depending on the type of data (e.g. use areas or metasites) selected for the species.
Contributors and References List of data contributors and references for data that were used to generate the products displayed in the Map window.
Layer drawing and symbology options You can change the symbology (e.g. color, line type) for the products displayed in the Map window.
Options You can control mapping options (e.g. projection) and additional layers (e.g. Exclusive Economic Zones) to draw on the map.
Download Goes through the download wizard to export the products displayed in the Map window. You can choose download format, either PDF or ESRI file geodatabase.

Filtering Panel

After a species is selected, the Filtering Panel is populated with additional criteria. They may be selected or deselected to change the viewable results on the map. The Activity and Population selection windows will scroll if there are more selections than what are visible. To select a single activity or population, single click on a value. To select more than one value, hold down the control (Windows) or command (Mac) key while clicking on each value. The map will show results that match all the selected criteria.

Displayed results are MiCO Nodes or Corridors, generated with standard Kernel Density Estimate methods (see the MiCO Methods overview for more information on how MiCO Nodes and Corridors are generated).

MiCO Nodes are areas of use for a particular activity, e.g. a feeding area, a breeding area, or a wintering area. MiCO Corridors are areas of migrating individuals. If the Show Core Use option is selected, a smaller area representing the “core” density of the node or corridor is displayed.

Use the Globe icon to export map results to a KML file for viewing in Google Earth. Use the Trashcan icon to remove a species/story from the map.

Results Panel


Interactive summary charts and their underlying data for the Use Areas, Metasites and Corridors are included on the Results tab. Specifics like the number of animals and the active months are displayed. Clicking on a segment of a pie chart will highlight the corresponding Use areas or Metasites on the map. Horizontal bars in the latitudinal leap chart are also clickable. A second click will turn off the highlighting.

Contributor and References Panel


Information about the data used to create the MiCO Use Areas and references for the Metasites and Corridors are listed in the Contributors and References Panel. All data contributors are acknowledged and information about their contributed datasets are shown. The list is updated based on the data shown on the map.

Mapping Options Panel

Options in the Mapping Options Panel allow changing the map projection, changing where the legend is displayed, select or deselect contextual data layers for display, and allow for changing the basemap. Toggling on the EEZ layer allows for filtering data by EEZ back on the main map. Once EEZ data is displayed, click on a zone to activate it. A popup window allow for identifying MiCO data that intersects or is contained within the EEZ.

Clicking on the “More Layers…” link will bring up a window to enter the URL of an external ESRI webservice layer to add.

Download Wizard

Download Wizard allows you to go through simple steps to download the data on the map as PDF or ESRI file geodatabase (zipped).

The PDF report contains the map and a summary of the products displayed in the map. You have the option of exporting the whole map, or of drawing a rectangular polygon extent on which to report. If multiple reports are to be exported for the same extent, but for different results, the user can select the “Previous extent” option for consistency. Click on “Map, Chart & Summary as PDF” button to generate the PDF, which will open in a new browser tab (if it doesn’t appear, check that your browser does not block pop-ups).
Sample PDF (Basking Shark metasites & corridors) —

The file geodatabase format may include multiple file geodatabases in a zipped file, depending on what products are displayed in the Map. There is no option to define the extent. The file geodatabase always include the products currently on the Map according to your criteria. Click on “Map Features as ESRI FGDB” button to generate a zippe file of the file geodatabase(s).

Field Descriptions

Metasites / Sites / Nodes (node.gdb – node_exported)
OBJECTID Internal unique ID of the area
prod_id ID of the area
cntr_lv Control level. Null for metasites or sites that came from literature reviews. 90=Use Area; 25:Core Area; Other values are not visualized on the MiCO System.
activity Species activity assigned to the area
description Description of the area
Type Type of the area. METASITE / SITE / NODE
cntrd_lt Latitude in decimal degrees
cntrd_ln Longitude in decimal degrees
n_ndvdl Number of individuals
radius Estimated radius of the site in degrees
method Method used to the study.
came_from Data came from either literature reviews or KDEs
species_code Species code
release_stage Release stage of the data. 2: Public; 0: Private
zotero_id Zotero ID for the literature reviewed.
review_id Internal ID of the literature review.
activity_code Code of the activity
metasite_id Metasite ID if the site belongs to a metasite.
children Child sites of the metasite
radius_m Estimated radius of the site in meters
sampling_technology Sampling technology described in the literature.
population_identifier Population identifier
years Years reported in the literature.
months Months reported in the literature.
life_stage Life stage of the animals with the number of individuals. May have multiple codes in JSON format. See the codes below.
sex Sex of the animals with the number of individuals. May have multiple codes in JSON format. See the codes below.
version Version of the data
last_updated The date the data was last updated.
Metaroutes / Routes / Connections (corridor.gdb – corridor_exported)
OBJECTID Internal unique ID of the area
source prod_id of the source
target prod_id of the target
type Type of the line. METAROUTE / METACONNECTION / Corridor
weight The number of individuals that represent the corridor.
start_x Longitude of the source
end_x Longitude of the target
start_y Latitude of the source
end_y Latitude of the target
method Method used to trace the animals. T: Telemetry; MR: Mark-recapture; G: Genetic
came_from Data came from either literature reviews or KDEs
num_trips Number of trips
num_individuals Number of individuals
species_code Species code
direction Direction of the line. 0: Not specified. 1: One way from source to target. 2: Both ways between source and target.
release_stage Release stage of the data. 2: Public; 0: Private
zotero_id Zotero ID for the literature reviewed.
review_id Internal ID of the literature review.
source_activity Species activity assigned to the source
target_activity Species activity assigned to the target
metasite_source The source of the metasite
metasite_target The target of the metasite
children The child sites of the metasite
source_radius The radius of the source in decimal degrees
source_radius_m The radius of the source in meters
target_radius The radius of the target in decimal degrees
target_radius_m The radius of the target in meters
version Version of the data
last_updated The date the data was last updated.
Use & Core Areas (kde.gdb – kde_exported)
OBJECTID Internal unique ID of the area
prod_id ID of the area
activty Species activity assigned to the area
dscrptn Description of the area
cntr_lv Control level. 90=Use Area; 25=Core Area; Other values are not visualized on the MiCO System.
Type Type of the area. Always “Corridor”
taxon_group Taxonomic group of the species
species_code Species code
common_name Species common name
scientific Species scientific name
site_name Name of the area
colony_name Colony name for seabirds
cntrlvl Same as cntr_lv as an integer.
age Life stage of the species. May have multiple codes. See the codes below.
sex Sex of the species. May have multiple codes. See the codes below.
device The device attached to the animal.
area_geo The area in square meters.
sort_order Internal use.
last_updated The date the data was last updated.
activity_code Code of the activity
version Version of the data
release_stage Release stage of the data. 2: Public; 0: Private

Life stages

A: Adult
AB: Adult Breeding
ABG: Adult Brood-guard
ABG-BG: Adult Brood-guard
ABG-CB: Adult Chick-brood
ABG-CG: Adult Chick-guard
ACR: Adult Chick-rear
AI: Adult internesting
AIN: Adult Incubation
APG: Adult Post-guard
AS: Adult Sabbatical
AS-PB: Adult Post-breeding
AS-S: Adult Sabbatical
C: Chick
CA: Calf
COY: Cub of the year
I: Immature
J: Juvenile
NB: Newborn
NH: Neonate/post-hatching
SUB: Subadult
UNK: Unknown
YL: Yearling

Sex

M: Male
F: Female
U: Unknown

System Design

The MiCO System data and mapping tools are built with cutting-edge technologies, software and services. The features require a modern browser such as Chrome, Firefox, Safari or Edge.

The Software Stack

  • ESRI ArcGIS
    MiCO Team uses the ESRI ArcGIS suite intensively to analyze species movements and connectivity and produce data products. ArcGIS is also used for summary analysis and preparing data for visualization with the online mapping tools.
  • ESRI Enterprise Geodatabase
    Once the MiCO products such as distribution polygons are generated, they are incorporated as feature classes in an Enterprise Geodatabase built on top of a PostgreSQL database.
  • ESRI ArcGIS Server & ESRI Javascript API
    The MiCO products stored in the Enterprise Geodatabase are served as dynamic map services through ArcGIS Server and visualized online using ESRI Javascript API. The EEZ layer is served as a tiled cache service due to its large size.
  • ESRI ArcGIS Online
    Some background layers of the map are available through ESRI ArcGIS Online. It is also used as the Geometry Engine (e.g. to change the geographic projection of polygons).
  • PostgreSQL
    Non-spatial data such as species profiles and attributes of the MiCO products are stored in a PostgreSQL database. The Enterprise Geodatabase and the non-spatial PostgreSQL database are integrated to produce summaries and statistics of the MiCO products.
  • Javascript with EXTJS 4
    While the main part of the Mapping Tool is based on ESRI Javascript, other parts of the Tool are built using pure Javascript and the EXTJS 4 library. Some dynamic features, such as the export of the map image, are employ the latest canvas and SVG technologies supported by modern browsers. Due to the interactive features of the tools, the code base has passed 15000 lines.
  • Apache & PHP
    Non-spatial visualization of the Mapping Tool is implemented by dynamic (asynchronous) connections between Javascript and the backend PHP scripts over Apache. The major task of PHP scripts is to make non-spatial queries to the PostgreSQL database, format the extracted data and send them to the browser. The export feature that allows you to save the map image and information as a PDF is built with FPDF library.
  • D3
    Statistical visualization, interactive charts, and graphs are generated using the D3 Javascript library.
  • WordPress
    General site content is managed with WordPress.

Currently, there are two components to the MiCO data tools; Overview and the Mapping Tool. The Overview  is both a summary cover page of data products and a literal cover page, as it lifts like a curtain to reveal the advanced Mapping Tool.  It provides an at-a-glance view of the MiCO products for a quick understanding of what MiCO provides. Behind the curtain, the Mapping Tool allows for advanced filtering and spatial exploration of the MiCO data. As you work, the Overview keeps track of selections in the Mapping Tool to produce snapshots of the map state.

System configuration

Acknowledgments