Best practices: Collecting Data with MicaSense

RedEdge and Parrot Sequoia

December 19, 2017 15:21

MicaSense RedEdge and Parrot Sequoia enable you to capture great data. This
article offers some basic guidelines to provide the best results. It covers the following
topics:

 Mission planning, to ensure proper overlap

 When to best capture data to minimize shadows
 How to properly use a calibrated reflectance panel; and
 The effects of ambient light conditions on your data

Mission Planning
Good data starts with good mission planning. The area to be captured should be larger
than the actual field of interest so that there is sufficient data all the way to the edges of
the field. Set up a grid survey using your system’s mission planning utility. One additional
flight track should be configured on either side of the field. Also be sure there is sufficient
space at the end of each flight track for the aircraft to re-align for the next pass. This is
particularly important for fixed-wing aircraft platforms.
Overlap

When setting up the mission, pay careful attention to the distance between tracks,
the sidelap, and the distance between successive captures, the frontlap. Both of these
should be configured to yield a 75% overlap.

By 75% overlap, we mean that as the aircraft travels along a flight track, each following
image overlaps the previous by 75%, both in the forward direction as well as the side
direction on the parallel track.

Flight Planners and Camera Parameters

Use your system’s mission planning utility to set up the flight plan at 75% overlap. It is
essential that the mission planner you use supports your camera's specific
parameters. While the specific method will vary depending on your system, be sure you
select RedEdge-M, RedEdge, or Sequoia as the camera type, and make sure to
configure the camera's overlap mode as the trigger.

If using Atlas Flight, there is no need to set any parameters as it is already configured for
both cameras. Otherwise, camera parameters are available on our knowledge base
for RedEdge-M, RedEdge and Sequoia. The parameters are set up for a camera that is
positioned horizontally (landscape), so if the camera is positioned vertically (portrait) in
your integration, you will need to reverse the width and height specifications.

You can check that your mission planner has the correct parameters for RedEdge by
comparing it to the example flight plan below, which is set up for an altitude of 122 meters
and 75% overlap. If you create the same flight plan, the front-lap spacing should be 20
meters and the track spacing should be 26.6 meters:

If you have any doubts about setting up your mission, please refer to the MicaSense
Knowledge Base or contact us.

Speed and Altitude

Keep in mind that the frontlap along the flight direction also depends on the flight speed
and altitude above the ground. RedEdge and Sequoia can capture images quickly, as fast
as once a second. However, there are combinations of flight altitude and flight speed that
will not yield proper frontlap. As this graph shows, slower speeds should be used at lower
flight altitudes.

Sample overlap chart for RedEdge

Proper overlap is extremely important for good quality data. If the overlap is insufficient,
the outputs are likely to have defects such as blotchy artifacts or errors in the image
alignment.

As you create a flight mission, if the field to be mapped requires more than one flight to
fully cover, the flights should overlap by at least one pass.

When setting up a flight mission over fields that have rows planted in a specific direction,
the flight tracks should be oriented such that they are perpendicular to the rows if possible.
This will provide the most consistent data output for this type of field.

When imaging tall trees or crops, the height of the tallest objects should be used for flight
planning. it's important to consider the altitude of the forest canopy when calculating
overlap.

Results of poor overlap

Best Time for Capture
The time of day for capturing data is also important. Flights should be performed within two
and a half hours of local solar noon.

By doing this, the output does not suffer from deep shadows, which can significantly affect
the multispectral results. Shadows not only obscure some vegetation but can also affect
values of vegetation indices over areas that are fully or even partly shaded.

Avoid sunspots

The only exception to flying at solar noon would be if you were to fly in very sunny
conditions where, if the sun were directly overhead, it would produce bright sunspots in the
data you capture. In cases like this, we recommend flying while the sun is at a lower angle.
Calibrated Reflectance Panels
To create reflectance-compensated outputs, an image of a calibrated reflectance panel
should be captured immediately before and immediately after each and every flight. This
applies even if a single field is covered in multiple flights – that is, always capture a panel
image before and after each flight for that field.

Before capturing the panel, ensure that the camera has a good GPS fix so that the panel
images will contain appropriate location and time information. This is important for post
processing.

The panel should be placed flat on the ground, far away from any objects that could affect
the light that illuminates it. Stand in front of the panel such that the sun is at your back.
Then take a large step to the left or to the right. Hold the aircraft at chest level and point
the camera such that the panel is centered in the field of view and such that there are no
shadows on the panel. The camera should be directly overhead the panel if possible, or
offset slightly to prevent shadows.
Shadows on the panel will invalidate the reflectance compensation readings. Also, if light
is reflecting onto another object and then onto the panel, the readings will be inaccurate. In
this example, light is reflecting off the clothing of the person holding the aircraft and then
onto the panel.

When capturing the panel image using RedEdge, use either the Capture button in the
camera’s WiFi interface page or push the physical button on the front of the
camera. External trigger mode, timer mode, or overlap mode should not be used for
panel captures. These modes will cause saturation of the panel images.

Sequoia firmware version v1.1.0 and higher comes with a "radiometric calibration" shot
mode available via the WiFi interface which takes 3 different exposure captures in order to
avoid saturation.

REDEDGE CAPTURE MODE

SEQUOIA RADIOMETRIC CALIBRATION MODE (v 1.1.0 +)

Ensure that the panel takes up at least one third of the image width, and that the QR code
and serial number label are visible in the image.
Ambient Light Conditions
In order to collect reflectance-compensated results, the light conditions at the time of
capture should be consistent throughout any one flight. Clear sunny days as well as light
overcast days in which the ambient light is not changing are best. Avoid capturing data in
partly cloudy days with rolling clouds.

Data captured in cloudy conditions, where the sun is partly or fully obscured for portions of
the flight, will suffer from anomalies such as the ones shown in these images.
The accuracy of the reflectance values for data captured in these conditions is
questionable. Additionally, these defects not only affect the color image but can also affect
the vegetation indices.

If capturing data in partly cloudy days is unavoidable, make sure that at least one
reflectance panel image is captured in bright conditions.

Feature Variability
Including unique features and variability in your captures helps increase the accuracy of
your output mosaic. While it may not be feasible to place unique features everywhere
throughout your field, there are other positive actions you can take. One simple way to
include variability in your data would be to make extra passes beyond your field, as
outlined in the overlap section. The edges of the field are often feature-rich (roads,
structures, cars, and others) while the center of a cornfield is quite homogeneous.
Including the edges helps to tie it all together.

Nadir
It is extremely important to ensure that the camera is pointing at nadir (straight down) or as
close to nadir as possible (even if you are flying over sloped terrain). There are several
gimbal options available from integrators. If you are not using a gimbal, be sure to account
for the tilt of the aircraft as it flies forward and adjust the camera's position accordingly.

Sloped Terrain

If you are flying over sloped terrain (such as a vineyard), maintain an altitude which is
constant relative to the slope/ground, and fly perpendicular to the field. If "terrain following"
is not possible, split the field into multiple flights, choosing an altitude above the highest
elevation. Also, choose a time of day to minimize shadows (this may be different than solar
noon).
Support
Following these guidelines will help yield the best data output. For further information,
access our Knowledge Base, where you can find the latest version of user manuals and
other helpful documentation. Or send us an email.
An overview of the available layers and indices in
Atlas
November 02, 2017 16:39

Table of Contents

 NDVI
 CIR
 NDRE
 Chlorphyll Map
 OSAVI
 DSM

NDVI (Normalized Difference Vegetation Index)

Uses

 plant vigor
 differences in soil water availability
 foliar nutrient content (when water is not limiting)
 yield potential

Summary

As plants become healthier, the intensity of reflectance increases in the NIR and
decreases in the Red, which is the physical basis for most vegetation indices. NDVI values
can be a maximum value of 1, with lower values indicating lower plant vigor. Therefore, 0.5
typically indicates low vigor whereas 0.9 indicates very high vigor. NDVI is also effective
for distinguishing vegetation from soil. NDVI is recommended when looking for differences
in above-ground biomass in time or across space. NDVI is most effective at portraying
variation in canopy density during early and mid development stages but tends to lose
sensitivity at high levels of canopy density.

CIR Composite (Color Infrared)

Uses

 assessing plant health

 identifying water bodies
 variability in soil moisture
 assessing soil composition

Description

This layer is a color composite and not an Index. It is referred to as a Color Infrared
Composite because instead of combining Red, Green, and Blue bands (which is the
standard image display method you are accustomed to) we are combining NIR, Red, and
Green bands. NIR light is displayed as red, red light is displayed as green, and green light
is displayed as blue (R: NIR, G: RED, B: GREEN). This color composite highlights the
response of the Near-infrared band to crop health and water bodies.

Healthy vegetation reflects a high level of NIR and appears red in CIR layers. Unhealthy
vegetation will reflect less in the NIR and appear as washed out pink tones, very sick or
dormant vegetation is often green or tan, and man-made structures are light blue-green.
Soils may also appear light blue, green, or tan depending on how sandy it is, with sandiest
soil appearing light tan and clay soils as dark tan or bluish green. This is also highly useful
in identifying water bodies in the imagery, which absorb NIR wavelengths and appear
black when water is clear. Since this is not an index, as stated above, there is no color
palette to select. The colors you see are a result of additive mixture of NIR, Red, and
Green wavelengths at each image pixel.

NDRE (Normalized Difference Red Edge)

Uses

 leaf chlorophyll content

 plant vigor
 stress detection
 fertilizer demand
 Nitrogen uptake

Description

NDRE is an index that can only be formulated when the Red edge band is available in a
sensor. It is sensitive to chlorophyll content in leaves (how green a leaf appears),
variability in leaf area, and soil background effects. High values of NDRE represent higher
levels of leaf chlorophyll content than lower values. Soil typically has the lowest values,
unhealthy plants have intermediate values, and healthy plants have the highest values.
Consider using NDRE if you are interested in mapping variability in fertilizer requirements
or foliar Nitrogen, not necessarily Nitrogen availability in the soil.

Chlorophyll has maximum absorption in the red waveband and therefore red light does not
penetrate very far past a few leaf layers. On the other hand, light in the green and red-
edge edge can penetrate a leaf much more deeply than blue or red light so a pure red-
edge waveband will be more sensitive to medium to high levels of chlorophyll content, and
hence leaf nitrogen, than a broad waveband that encompasses blue light, red light, or a
mixture of visible and NIR light (e.g. a modified single-imager camera).

NDRE is a better indicator of vegetation health/vigor than NDVI for mid to late season
crops that have accumulated high levels of chlorophyll in their leaves because red-edge
light is more translucent to leaves than red light and so it is less likely to be completely
absorbed by a canopy. It is more suitable than NDVI for intensive management
applications throughout the growing season because NDVI often loses sensitivity after
plants accumulate a critical level of leaf cover or chlorophyll content.

Chlorophyll Map
Uses

 detect chlorotic crops

 stress detection
 identify vigorous, healthy crops
 estimate chlorophyll content
 estimate N content if you know that N is limiting

Description

The Chlorophyll Map is a layer that is less sensitive to leaf area than NDRE. This
layer isolates the chlorophyll signal from variability in leaf area as a function of changes in
canopy cover. It has a physiological basis which takes into account the relationship
between canopy cover and canopy nutrient content.

The Chlorophyll Map is especially sensitive to well gathered and well calibrated
data. Non-plant pixels are excluded and shown as transparent, which in some cases
results in plant pixels also being omitted. This layer is less useful for row crops and more
useful for vineyards and orchards, as the dense canopy is better at differentiating the
Chlorophyll signal.

OSAVI (Optimized Soil-Adjusted Vegetation Index)

Uses

 differentiate soil pixels

 related to LAI at some levels where NDVI saturates
 accounts for non-linear interactions of light between soil and vegetation
 used as a structural index for some combined indices designed for chlorophyll detection

Description

OSAVI maps variability in canopy density. In addition, it is not sensitive to soil brightness
(when different soil types are present). It is robust to variability in soil brightness and has
enhanced sensitivity to vegetation cover greater than 50%. This index is best used in
areas with relatively sparse vegetation where soil is visible through the canopy and where
NDVI saturates (high plant density).

OSAVI is a special case of the Soil Adjusted Vegetation Index (SAVI). OSAVI was
developed by Rondeaux et al. in 1996 using the reflectance in the near-infrared (nir) and
red (r) bands with an optimized soil adjustment coefficient. The soil adjustment coefficient
(0.16) was selected as the optimal value to minimize NDVI's sensitivity to variation in soil
background under a wide range of environmental conditions. OSAVI is a hybrid between
ratio-based indices such as NDVI and orthogonal indices such as PVI. SAVI has a default
soil-adjustment factor of 0.5; however, it is recommended to use 0.16 as implemented in
OSAVI. Like any normalized difference index, OSAVI values can range from -1 to 1. High
OSAVI values indicate denser, healthier vegetation whereas lower values indicate less
vigor.

DSM (Digital surface Model)

Uses

 estimate relative crop volume

 identify surface properties
 model water flow & accumulation

Description

DSM is a digital model representation of a terrain's surface. DSM represents the

elevations above sea level of the ground and all features on it. A DSM is a gridded array of
elevations. it is a layer symbolized by a gray color ramp, special effects such as hill-
shading may be used to simulate relief. DSMs can be used to study surface properties and
water flow.
A digital surface model (DSM) is usually constructed using automatic extraction algorithms
(i.e. image correlation in stereo photogrammetry). DSM resembles laying a blanket on your
imagery. It represents top faces of all objects on the terrain, including vegetation and man-
made features, and highlights the different elevations of the features

How do I work with MicaSense GeoTiff's in

QGIS and create a PDF report?
May 01, 2017 19:11

Now you can print and create basic PDF reports from Atlas: Printing from Atlas

Using ArcMap? Check out the ArcMap tutorial here.

Optional Step - Download QGIS

To download QGIS, simply go to (https://www.qgis.org/en/site/forusers/download.html) and

download the latest version that is appropriate for your Operating System. Follow the steps
in the QGIS setup to install your version. Then, open QGIS.

1. Download GeoTIFF from Atlas

Go to https://atlas.micasense.com/data, then click the for the image set(s)

you are interested in.
2. Drag and Drop Data into QGIS

Drag the downloaded GeoTIFF into QGIS. After it is loaded into QGIS, it should appear in
your “Layers” menu.

3. Set the Layer Properties

Set the layer properties by double-clicking on the layer, then setting the red band to “Band
3”, green band to “Band 2”, and blue band to “Band 1”. Set the cumulative count cut to 0.2-
99.8% and click "Load". Then, look at the band rendering min/max values for all bands and
find the greatest max value. Copy and paste that value as the max for all bands. Now find
the smallest minimum value and copy and paste that as the min value for all bands. Lastly,
to ensure that there is less aliasing when zooming in and out of the image, set the
resampling to Nearest neighbor for zooming in, and Average for zooming out. Then, click
“Apply”.
This will set the band rendering of the GeoTIFF so that the RGB colors are more similar to
what you see in ATLAS.

4. Calculate NDVI and NDRE with the Raster Calculator

NDVI and NDRE are the vegetation indices seen in ATLAS currently, but there are many
more that can be calculated from a 5-band GeoTIFF. For more information on these
indices, we recommend reading “Active Ground Optical Remote Sensing for Improved
Monitoring of Seedling Stress in Nurseries” (http://www.mdpi.com/1424-8220/10/4/2843).
The formulas for calculating the spectral indices found in ATLAS are as follows:
To calculate spectral indices in QGIS, use the raster calculator (Raster>Raster Calculator).
Double click the raster bands to add them into the expression box. Then, use the operator
buttons to add parentheses, addition, subtraction, and division symbol (Note: Do not
simply type in the necessary symbols, you must use the operator keys for this to work
correctly). Be sure to check that the extent of the layer is correct. If needed, click the
“current layer extent” button to adjust the extent to match the current layer. Lastly, choose
the output file and layer name by clicking the “…” button next to the Output Layer box.

5. Change Layer Color Scales to Match Atlas Output

You should see something similar to this in QGIS when your newly created layer finishes
calculating.
To change the color scale of the layer, double click on the layer to open the layer
properties. Click on the dropdown “Render Type” menu, and select Singleband
pseudocolor. Change the color scale to what you believe to be most appropriate for your
data, then click “Classify”.

To Recreate the NDVI Map Color Scale Seen in ATLAS…

Click the dropdown “Generate new color map” menu, and select RedYlGn. Change the
Mode to Equal Inverval and Classes to 11. Set the Min to 0.5 and Max to 1, then click
“Classify”. Double click on the red box next to the 0.5 value to change the color. Set the
Opacity to 0%, then click OK.

In the Layer Properties, click Apply. The final layer properties window should look like
similar to this:
Create a PDF Report in QGIS
1. Open Print Composer

Using the Menu Tool Bar seen at the top of your QGIS window navigate to Project>New
Print Composer, or type CTRL+P. A window should pop up prompting you to give your
print composer a name, you may name it or let QGIS auto-generate a name for you. This
name is what your composer file (Not PDF) will be saved as so that you can go back and
edit it later. After this, the composer screen should pop up.

2. Change Page Size and Margins

Change your page side and margins to fit your preferences using the menu tool bar to
navigate to Composer>Page Set Up (Or, simply type CTRL+Shift+P).

3. Add Map to Composer

Add your map by navigating to Layout>Add Map. Drag a box on your composer window
that is the appropriate size for your map.

Then, from your QGIS window (Not composer window), zoom in and out to change the
extent of your map. Back on the Composer window, under Main properties, click “Set to
map canvas extent”. Repeat this until the composer reflects your desired map extent.

4. Add Scale Bar

Add a scale bar to your map by navigating to Layout>Add Scalebar. Click the location on
the map where you want to place your scalebar. You can also drag and move your
scalebar as you wish.
5. Add Legend

Add a Legend to your map by navigating to Layout>Add Legend. Click the location on
the map where you want to place your legend. You can also drag and move your legend
as you wish.

6. Add Text

Add a title, note, or any form of text to your map by navigating to Layout>Add Label. Click
the location on the map where you want to place your text, then resize the box so that it
has the appropriate margins. When you click on your map, the item properties menu
should display automatically:

7. Add a Logo or Other Relevant Images

Add an image to your map by navigating to Layout>Add Image. Click the location on the
map where you want to place your legend, and drag such that the box is the desired size.
The item properties should appear to the left of your map. Select the image you wish to
use by changing the Image Source by clicking “…”. Change the resize mode and
placement as you see fit. After you are satisfied with your image, you can move and resize
the image within the composer window.

8. Save as PDF

Save your composer as a PDF by navigating to Composer>Export as PDF. Select the file
name and location you wish to save your PDF in, then click “Save”.