Agisoft Photoscan Crash Course (v. 1.0.

2)
*Updated version for Photoscan 1.1 is finally here*
A not-so-quick tutorial in using Photoscan to process a single photoset in Agisoft Photoscan
Professional version 1.0 (1.0.2 or 1.0.3), for Photoscan version 1.1 please see the updated
tutorial.
I have written this for various research groups at the University of Oregon, Oregon State
University, and Dartmouth College. I hope that this will help others get started as well. I also
plan to add screen shots to this eventually, but for now this will have to do.

Photo Prep
1. Eliminate any blurry, out of focus, random photos from your photoset
2. If you has GPS track data for you photos, use a program like GeoSetter to geotag your photos
before processing.
a. With geotagged photos, the coordinates are usually Lat/Long (in degrees); use the convert tool
in the ground control pane to convert to UTM.
b. Never use geotagged photos as the sole source of georeferencing information. The errors in
consumer grade GPS units (handheld or in camera) is too great for anything more than helping
with photo alignment.
3. Make sure you have a camera calibration file ready to go for your camera
a. Agisoft has a tool for this on their website
b. When calibrating in Agisoft Lens be sure that all of the variable boxes are checked

Photo Alignment

i.
ii.
i.
ii.
iii.
i.
ii.

i.
ii.
iii.

1. Load your photos

a. Apply the camera calibration file to all of the photos (ToolsCamera Calibration)
2. Align Photos Settings:
a. Accuracy:
High: is best for smaller photosets
Medium: is best for larger photosets
b. Pair Selection:
Disabled: default, works for most datasets
Generic: I use this one if Im having trouble getting photos to align
Ground Control: If your photos are geotagged, this will use the GPS positions to speed up
processing.
c. Advanced:
Point Limit: 40,000 is default. Smaller numbers can speed up processing, but you run the risk of not
having enough points to align photos.
Constrain features by mask: You can use masks to exclude parts of the images you do not want to
model, check this box if you have masks.
3. Fixing misaligned/unaligned photos
a. After the initial pass of photo alignment, there may be photos that are misaligned or unaligned.
You can force the program to try again, usually this works (but not always).
Select all of the photos that are causing trouble, right-click and select Reset Alignment
Right-click again, select Align Selected Cameras
If that does not work, select a smaller batch of problem photos and try again working in small
batches.

iv. If none of that works, there is not a whole lot you can do but disable or exclude the photos that will
not align.

Georeferencing

i.
ii.
iii.
iv.

i.

1. Prep your control point data

a. Double-check your projection and vertical datum, do any conversions outside of Photoscan.
b. Load your data points into Excel and delete all but the NAME, LAT(Northing), LONG(Easting),
ELEV to simplify things.
c. Save as a text file (tab delimited)
d. Use the Import tool in the Ground Control pane, set the import settings, say Yes to all when it
asks to add points.
e. If you import a larger file, you should delete any points that are not present in the photoset.
2. Set your projection with the Settings, the other settings are default
3. Find the first photo with a ground control point
a. Double-click the photo to open it, zoom in on the control point, right-click on the center of the
control point marker, select Place Marker and select the appropriate marker.
b. Find the next photo with the same GCP as the first, set the marker.
Once you have a marker placed in two photos the software starts to guess where they should be in
other photos.
Right-click on the marker you have been working on, select Filter Photos by Marker. This will show
just the photos that the marker is in.
Click through all of the photos and place the markers.
If a photo has a marker flag in it, but the GCP is not visible
1. You can leave it as a gray flag and it will not be used, or
2. You can right-click on it and Remove Marker
c. In the photos pane, select Reset Filter to get back to the full photoset.
d. Repeat the above steps for the next two GCPs
4. After you have three GCP markers set, you can Update the georeferencing in the ground
control pane
a. This will roughly georeference the model and make finding the remaining GCPs easier
b. If your first three points are close together, this may not work very well
In this case you will likely have to manually find and mark an additional GCP
5. Right-click on the next GCP in the list and Filter Photos by Marker
a. Run through all of the photos and place the markers
b. Update again to refine the georeferencing
c. Repeat this step for the rest of the GCPs
6. Double-check that all of your GCP markers are placed
a. Right-click on all of the GCPs and Filter Photos by Marker
b. Double-check that all of the photos have little blue flags above them in the photo pane.
c. Update one last time

Optimize the alignment

1. Double-check that you have a camera calibration applied to all of the photos
2. Click on Optimize in the ground control pane
a. Make sure the Fit k4 box is checked
b. This optimizes the camera alignment based on the camera calibration and control points
3. Check your error for each GCP
a. In the georeferencing pane, the point with the worst error is highlighted in red
i. You can also click on View Errors to view the X, Y, and Z components of the error

b. If you have points with errors that are higher than you would like, you can uncheck the box on
the left to exclude it from the georeferencing calculations
c. Update the georeferencing, repeat for any other bad points if necessary
d. If you change exclude a lot of points, re-optimizing is a good thing to do

Building Dense Point Clouds

i.

ii.
iii.
i.

1. Check the bounding box (the light gray box with a red bottom) size and orientation
a. Use the Resize Region and Rotate Region tools on the toolbar if the bounding box looks like it
is going to cut off any parts of the model
2. Settings
a. Quality:
This is the super memory intensive part of the process, photosets that are large (lots of photos) can
take a long time to complete. Too many photos cause the program to run out of memory. The
quality thats achievable and the time it takes depend on your processor (CPU), RAM, and video
card (GPU)
High: great for smaller photosets (up to 150 photos)
Medium: good for larger datasets (over 150 photos)
b. Advanced
Depth Filtering: Aggressive (default), limits points that are too far from the surface. For vegetation,
this may need to be relaxed a bit.

Point Cloud Editing

1. If there are any points in the dense point cloud are outside of the envelope you wish to export,
you can manually delete them
2. Use the Rectangle Selection, Circle Selection, or Free-from Selection tools on the toolbar to
select and delete errant points

Build Mesh
i.

ii.
i.
ii.
i.
ii.
i.
ii.

1. Settings
a. Surface Type:
Height Field: only builds a mesh surface orthogonal to the reference system Z-axis (i.e. no undercuts
will be modeled). This is the fastest mesh procedure and excellent if DEMs are going to be your
final product.
1. For geography applications, a height field would normally be modeled orthogonal to the Z-axis of
the coordinate system. In Photoscan, the height field is actually modeled against the orientation
of the bounding box (the light gray box with a red bottom) of the model. You can run this Python
script (**Align Bounding Box Tool**) in the console to align the bounding box to the reference
system. You will need to
Arbitrary: Will model every nook and cranny of the object. Best for oblique imagery, when point
clouds or complex mesh surfaces are going to be the final product.
b. Source Data:
Dense cloud: default
Sparse cloud: You could use this, but I am not sure why
c. Polygon Count: The number of polygons that the model will be decimated to after processing.
The software has High, Medium, Low values
Or you can specify a custom number (entering 0 will not decimate the final model)
d. Interpolation
Enabled: default, will interpolate over small holes in the surface
Extrapolation: will leave holes in the final surface where there are no dense points
e. Point Classes:

i. There is a point classification tool in Photoscan. If you used it to classify the dense point cloud, you
could specify which point classes you want use for the mesh.

Exporting DEM / Orthophotos

i.
ii.
iii.
iv.
v.
vi.
vii.
viii.
i.
ii.
iii.
iv.
v.
vi.
vii.
viii.

1. FileExport DEMExport TIFF/BIL/XYZ

a. Settings:
Choose your projection
Crop invalid DEM: checked by default
No-data value: Use -9999 for ArcGIS
Pixel Size: Photoscan estimates an appropriate pixel size, can be changed to match your
requirements
Split in blocks: segment the DEM into X by X rasters (only needed for large datasets)
Set boundaries:
1. Check the box and click Estimate, this limits extra no-data values on the edges
Write world file: not necessary if you export a TIFF
Choose your output location, file name, and type
2. FileExport OrthophotoExport JPEG/TIFF/PNG
a. Settings:
Choose your projection
Blending mode: Mosaic (default)
Enable Color Correction: not usually necessary, but if you need the color to be evened out feel
free to select this option
Pixel Size: same as above
Split in Blocks: same as above
Set boundaries: same as above
Write world file: not necessary if you export a TIFF
Choose your output location, file name, and type