ThruTracker User & Troubleshooting Guide
by ThruTracker Analytics
ThruTracker Quick Processing Guide
1. Create or Open a Project
- Launch ThruTracker → New Project or Open Project
- Name the project and set a save location
- Add videos (copy into folder or reference in place)
2. Configure Detection Settings
- Select your video from the Select Video dropdown
- Set or create a Configuration file for the video
- Adjust detection settings:
- Target Diameter — match to your typical target size
- Sensitivity — start at default (4), adjust if needed
- Target Polarity — lighter or darker than background
- Max Density — estimate peak targets per frame
- Gate — draw around your area of interest
- Exclusion Zone — mask out problem areas if needed
3. Test Settings
- Set a start frame with good activity → Test Current Settings
- Review the 60-frame clip for missed detections, false detections, and track quality
- Adjust and retest as needed
- Click Save and Advanced when satisfied
4. Process the Video
- Process Single Video or Process Multiple Videos
- Configure run outputs (track overlay, gate overlay, colorize)
5. Review Tracking Quality
- Go to Tracking Review → select a review video
- Check for missed targets, track jumping, splitting, or duplicates
- Review the Emergence-Rate Graph for expected exit patterns
- Reprocess with adjusted settings if needed
6. Classify Tracks (Optional)
- Use Load Tracks (low volume) or View All Tracks (high volume)
- Apply classification categories (Star, Good, Bad, Exit, Entry, etc.)
- Add comments as needed
- Generate review images if desired
- Save Classifications before closing
The chapters below cover each of these steps in detail.
Projects
When opening ThruTracker, you are prompted to create or open an existing project.
Project Creation
When working with a video set that has not yet been processed, select New Project on the welcome dialog when launching ThruTracker. If the dialog has been closed, you can create a new project by going to File in the top menu and selecting New Project.
Give your project a unique name that is easy to distinguish from other projects or runs. You can also specify a location where the new project folder will be saved. We recommend creating a dedicated folder within your existing video project directory to keep processing runs organized, particularly if videos will be processed across multiple runs.
Adding Videos to Projects
After entering a project name and selecting a file location, click OK to proceed to video selection. You can either copy videos directly into the project folder — which creates duplicates of the original files — or reference them in place, which links to the original files without modifying them. Additional videos can be added at any time by going to File in the top menu and selecting Add Videos.
Opening Projects
When working with an existing project, select Open Project on the welcome dialog when launching ThruTracker. If the dialog has been closed, you can open an existing project by going to File in the top menu and selecting Open Project.
The most frequently used files and folders are accessible directly within the application via buttons that open their respective locations after processing. For a full breakdown of the folders a project creates, see the Project File Structure appendix.
Detection Settings
The Detection Settings tab is where you can view videos included in your project and configure the settings ThruTracker uses to automatically detect and count targets.
Video Viewing
The main panel on the left in Detection Settings is the view window, where you can watch the selected video. You can adjust the playback speed (the default is 100%), loop the video for continuous replay, or jump to a specific frame. Use the zoom buttons to zoom in, zoom out, or fit the video to the screen. When zoomed in, click and drag with the left mouse button to pan around the image. Press the Play button or Space to play or pause the video. To step through frames one at a time, use the left/right arrow buttons or press the left/right arrow keys after clicking the timeline.
Basic Processing Guide
1. Video Selection
After adding videos to your project, use the Select Video dropdown to switch between them.
Configuration
A configuration is a saved settings file (a .yaml file in the project's config folder) holding the detection settings for a video or project. A default configuration is generated when a new project is created. Settings can be adjusted between videos, but changes are not saved unless separate settings files are created.
- Create one configuration per camera view. If your project includes videos with different camera views that need different detection settings, create a separate configuration for each view: click New, enter a name that clearly associates it with its video, and click OK to save.
- Switch and import. Use the dropdown to switch between configurations, or import configurations from other runs in the project.
- Edit is only needed when a settings file has been modified outside the application and needs to be reloaded.
Each time you switch your active video, select the matching configuration — this keeps video-specific settings from being overwritten by a single file shared across all videos in the project.
2. Target Diameter
When Target Diameter is selected, you can specify a diameter in pixels and left-click on the video to see a visual reference of a target at that size. If targets vary slightly in size but fall within a close range, choose a diameter toward the smaller end. If you are getting multiple detections on a single target (for example, one on each wing and one on the body), try increasing the target diameter or enabling Multiple Sizes. If real detections are being missed, try decreasing the diameter before adjusting sensitivity or max density.
If your targets form distinct clusters of large and small detections, or change size on screen (such as when flying toward the camera), enable Multiple Sizes. The single diameter field becomes a minimum diameter (for the smallest targets) and a maximum diameter (for the largest). Left-clicking the video with Multiple Sizes enabled shows the minimum diameter as a green circle and the maximum as a blue circle.
3. Sensitivity
Sensitivity controls how prominent targets must be against the background — specifically, the brightness contrast between a detection and its surrounding area. The scale ranges from 1 to 7:
- 1 — For very faint detections. May produce false detections or split tracks.
- 4 — The default. Suitable for the majority of runs.
- 7 — For detections with very high contrast to the background. May cause some detections to be missed.
If a test run shows too few detections and adjusting target diameter did not help, try lowering the sensitivity (1–3). If there are too many detections and adjusting target diameter did not help, try increasing the sensitivity (5–7).
Suppress Background filters out noise from parts of the scene that aren't moving. It is enabled by default and works best for stable footage from fixed cameras or scenes with consistent backgrounds. Consider disabling it if the camera is moving, the background is changing rapidly (such as clouds or fast lighting transitions), or if faint detections appear to be suppressed by the filter. This should be treated as a last resort — adjust target diameter, sensitivity, and max density first. Disabling suppress background may increase false noise detections. Note that this setting is automatically turned off when Max Density is set to its highest level (20+ Extreme).
4. Target Polarity
Target polarity defines the brightness of targets relative to the background.
- Lighter target on dark background — Select when targets are brighter than the background.
- Darker target on light background — Select when targets are darker than the background.
- Both lighter and darker — Select when the background is dynamic and targets may appear either brighter or darker.
5. Max Density
Max density represents the peak number of targets visible in a single frame.
- 1–5 animals per frame — For sparse, occasional targets.
- 6–20 animals per frame — For many targets visible at once.
Both settings automatically filter out noise and are recommended for most videos. For extremely dense footage, 20+ animals per frame (Extreme) is available. This mode trades noise filtering for the ability to handle very dense groups — it turns off Suppress Background and may increase false detections.
6. Bounding Box (Gate)
The bounding box, or gate, defines an area within the frame that ThruTracker uses to count target entries, exits, or boundary crossings. You can use a rectangle gate and specify boundary ranges from the top, bottom, left, and right edges, or draw a custom shape using the polygon tool. When drawing a gate, leave a small buffer around the edges of the area of interest. We recommend keeping the gate at least 5–10% away from any frame edge where you want to count boundary crosses — the program needs to detect a target on both the inside and outside of the gate to register a crossing.
7. Exclusion Zone (Mask)
The exclusion zone mask removes areas of the frame where you do not want detections to occur. This is useful for suppressing persistent false detections in areas such as timestamps, logos, and high-density swirling regions that generate many overlapping fragmented tracks (such as the mouth of a cave or building entrance). To draw a mask, set the brush size in pixels, click Paint to draw, and use Erase to refine edges. Click Finish when done. To remove all masks, click Clear Exclusion Mask.
Advanced Processing Guide
Advanced settings are used after finding the best-performing basic settings and are intended to further refine and isolate tracks.
8. Exclusion Size
Set the minimum detection diameter and check Filter detections smaller than this to remove detections below that threshold. Setting this a few pixels smaller than your smallest expected target provides a useful buffer. This is helpful when small noise detections — such as bugs or dust — persist after optimizing basic settings, or when you want to exclude distant, low-resolution detections in favor of close, clearly visible targets.
9. Exclusion Brightness
Exclusion brightness removes detections that fall below a minimum brightness threshold. This is particularly useful when counting exits from a thermal video in white-hot mode, where exiting targets are typically hotter and brighter than fly-bys or targets in open flight. Use Pick from Frame to sample the average brightness at a location in the video — zooming in first using the + button or Ctrl/Cmd + scroll wheel will improve precision. Set the slider to zero to disable this filter. Exclusion brightness can also reduce false detections on darker wing tips by focusing on high-temperature body detections.
10. Variable Size Tracking
Enable Variable Size Tracking (on by default) when detections gradually increase or decrease in size and are not distinct size clusters. Disable it if tracks are incorrectly joining or jumping between nearby detections.
11. Target Speed
Target speed tells ThruTracker how far a target can move between frames and still be treated as the same track.
- Default (3) — Suitable for most targets.
- Increase (4–5) — Use if fast-moving targets are being split into multiple tracks, after first checking target diameter, sensitivity, and max density.
- Decrease (2) — Use for very dense, slow-moving groups where tracks are jumping between nearby detections (extreme cases only).
Testing Current Settings
To evaluate your settings, navigate to a start frame with representative activity, specify the number of frames to test (default: 60), and click Test Current Settings. This plays a clip from the start frame with the gate overlay, frame number, and an in-frame track counter — note that this counts tracks currently visible in the frame, not cumulative tracks across the entire clip. You can adjust the playback speed for review (default: 50%). Enabling Bg_sub switches to a high-contrast view that makes faint detections easier to see.
You can adjust settings while the test clip is open, though clicking Exit Test Clip is recommended before redrawing the gate or editing masks. To undo all changes made in the current session, click Discard. Once the results look good, click Save and Advanced to proceed to full video processing.
Video Processing
Process Single Video
Before processing, confirm that the correct video and configuration file are selected. Click Process Single Video to generate tracks for one video in the project.
Process Multiple Videos
To process multiple videos in a single project using the same configuration, confirm that the correct configuration and all intended videos are selected before processing. Click Process Multiple Videos to begin.
Make Review Video From Last Run
To generate a custom review video without reprocessing the dataset, click Make Review Video From Last Run.
Configure Run Outputs
When processing a video or creating a review video, the Configure Run Outputs dialog opens.
- Track Overlay draws a colored box over each unique detection. A trail follows each detection, showing its trajectory from past frames as a series of circles. You can specify the number of circles per trail and the line thickness in pixels for both the trails and boxes.
- Gate Overlay Video produces a full processed video displaying gate counts, including exits, entries, and boundary crosses.
- Tracks-Only Video trims frames with no activity and adds a buffer before and after each track segment (default: 0.10 seconds).
- Colorize Output applies a color scheme to the review video for easier identification of individual target IDs:
- None (original) — Uses the standard color scheme of the recorded video.
- Inferno — Blue, purple, orange, and yellow from cold to hot.
- Hot (Iron) — Dark red to bright yellow from cold to hot.
- Turbo — Blue, green, yellow, and red from cold to hot.
- Greyscale — Black to white from cold to hot.
Tracking Review
Tracking Review is where you assess the quality of your detections and view the timeline of gate exits over the duration of the entire video. Review moments of interest to confirm that processing accurately identified your targets before deciding whether settings need adjustment for a rerun.
Selecting a Review Video
After processing your video, go to the Tracking Review tab and select the video you want to use to evaluate detection quality. Use the dropdown or browse to the overlay video folder to choose a review video.
Reviewing Detection Quality
Use the review video to confirm that:
- Targets of interest are being consistently detected.
- Individual tracks are maintained without track jumping or splitting.
- Each target is assigned a single track, with no duplicates.
- No real targets are being missed.
Emergence-Rate Graph
The emergence-rate graph displays the gate exit timeline across the full video, showing the number of exits per frame and the cumulative track count over time. Review the graph to confirm that the rate and pattern of exits match your expectations.
Classify Tracks
The Classify Tracks tab allows for additional track review and enables you to assign identification categories to tracks based on your project's requirements.
Track Review
Use the tools in the top menu to view and classify tracks.
1. Load Tracks
Select Load Tracks to review one track at a time. Navigate between tracks using the Previous/Next buttons or the left/right arrow keys. This mode is recommended for lower-volume videos and allows you to classify each track individually.
2. View All Tracks
Select View All Tracks to display all tracks simultaneously, along with options for selecting multiple tracks at once. This mode is best suited for moderate- to high-volume videos, or videos with a clearly defined exit of interest to separate from other tracks.
Classification Categories
| Category | Description |
|---|---|
| Star | A high-interest or high-quality track |
| Good | A good-quality track |
| Bad | Poor tracking, or a track generated from a false detection |
| Uncertain | Used when a complete single-detection track is difficult to distinguish from surrounding tracks; most common in high-volume, dense, or overlapping video |
| 1 — Exit | A detection exiting a roost |
| 2 — Entry | A detection entering a roost |
| 3 — Fly-by | A detection flying across a roost or area of interest |
| 4–9 (Unlabeled) | Custom categories you can define for your project (e.g., turns, conspecific interactions, investigative approaches) |
Additional Tools
- Clear All — Clears the currently loaded classification in Load Tracks mode.
- Comment — Adds a comment to one or more selected tracks.
- Make Review Video (Shown Tracks) — Use the Show dropdown to select which track categories to include, then generate a review video containing only the tracks of interest.
- Edit Number Labels — Add or rename custom classifications for labels 4–9.
- Save Classifications — Saves all applied categories, labels, and track reviews.
Generate Review Images
Select Generate Review Images to create still images for each track, showing the detection highlighted within the frame across the full track duration. You can specify a maximum number of images and the frequency at which images are captured. Navigate between images using the Previous/Next buttons or the left/right arrow keys. To open previously generated images, select Open Track Images from the menu.
Troubleshooting
Getting your first detections, and the common problems you fix by adjusting the core settings.
No Detections
ThruTracker looks for things that change from frame to frame, and the target settings (Target Diameter, Contrast sensitivity, Target Polarity, Max density) tell it how. The defaults work for most videos.
- Inverted target polarity. If you've set ThruTracker to find light targets on a dark background but your bats are the opposite (or vice versa), your targets of interest get filtered out and nothing is detected. Switch the Light/Dark setting — or pick "Both" if you're unsure.
- Target size too small. Size the Target Diameter circle to enclose the bat's brightest body. If larger bats are missed, increase the target diameter value (ThruTracker tends to handle targets slightly larger than expected better than smaller ones, though it can depend).
- Bats too faint (low contrast). A low-contrast bat blends into its background — a similar temperature in thermal video, or a similar color/brightness in regular video — so it barely stands out even as it moves. If the default contrast sensitivity is too strict to catch them, nudge it one step toward the “Maximum” end so fainter targets register.
Multiple Detections per Bat
ThruTracker marks each spot that stands out as its own target — and a bat's wings can stand out separately from its body. So if the expected target size is too small to cover the whole bat, you get one detection on the body plus extra ones on the wings, instead of a single box on the bat.
- Increase the target size (and consider Multiple sizes). Make the Target Diameter big enough to cover the whole bat, so the body and wing spots merge into one detection. If your bats appear at very different sizes in the video, turn on Multiple sizes under Target Diameter and set the largest with the blue Max diameter circle.
- Turn on Variable Size Tracking. This tells ThruTracker that a bat's bounding box is allowed to grow and shrink to match its actual size. It's especially helpful when bats are viewed from above or below, where the wingbeat cycle changes the apparent size dramatically, particularly for broad-winged bats. This is more of a problem in visible and near-IR video.
- Raise Exclusion Brightness. Wing detections tend to be cooler (dimmer) than the body, so a brightness floor can drop them.
False Detections
Because ThruTracker keys on things that move and stand out, anything else that does the same can look like a bat; foliage, insects, clouds, water ripples, even a bat's own reflection or shadow. These fixes help it tell that clutter apart from real bats.
- Start with the core settings. Get Target Diameter, Contrast sensitivity, and Max density dialed in first.
- Mask static noise. If the noise sits in a fixed spot that isn't near anything important (e.g., away from the gate crossing), paint over it with the Exclusion Zone so it's ignored.
- Turn on the Exclusion Size filter. Anything smaller than the orange circle is deleted, so size it to your insects, leaves, or static; just don't make it larger than the targets you want to keep.
- Use Exclusion Brightness. Great for false detections that stand out less than your bats (lower contrast, such as cooler than the body in thermal); a brightness floor drops them. This is often useful in thermal video, where the wings are less bright than the body.
- Keep people out of frame. Someone walking in front of the camera throws huge false detections. We're working on code to filter these "sasquatches" automatically; for now, prevent it at capture. ThruTracker may also warn you that part of the video has suspicious detections.
Zero or Negative Gate Counts
Counting is a separate step from detecting: ThruTracker only counts a bat when its track crosses the gate — passing from one side of the line to the other. So you can get plenty of detections but a count of zero when bats never actually cross the gate, or aren't tracked on both sides of it.
- Gate isn't across the flight path. A bat is only counted when it crosses the gate, so the gate has to sit across the bats' direction of travel (perpendicular to how they fly). If it runs along the flight path instead, bats fly parallel to it and never cross — lots of detections, no counts. Reorient the gate so it cuts across the flight.
- Gate touching the frame edge. A crossing only counts if the bat is tracked on both sides of the line. If the gate touches the edge of the frame, bats that leave right where the gate meets the edge are never seen on the far side, so they go uncounted. Pull the gate in from the edges so there's room on both sides.
- Negative counts can be real. A negative net isn't necessarily an error; it means more bats entered than exited. That's expected at dawn, when bats are returning rather than emerging, but it can also come from a gate drawn in the wrong position, which swaps the two directions. If you expected an emergence, check the gate.
- Near-zero can be genuine. If a lot of bats are swirling in and out of the entrance, the entries and exits can really cancel to near net zero. Check the entrance and exit activity in the video to confirm that's what's happening before treating the count as an error.
A crossing only counts when the gate sits across the flight path.
Finding the Action in Long, Low-Activity Recordings
These are the long recordings where bats only show up in short bursts, with a lot of empty video before and after. Scrolling through all of it to find the action is tedious and time-consuming, so let ThruTracker point you to the activity instead:
- Start from default settings, but set the polarity and draw a rough, generous gate.
- Run a test over a large chunk of the video (not tracks-only).
- Open the activity rate graph on the Tracking Review tab and scroll to a peak.
- See how the detections are performing there, and iterate as usual.
- Alternatively, run a test over a large chunk of the video (tracks-only) to create a composite of only periods where bats are detected on screen.
Fast, Blurry, Low-Contrast Bats
When this is your problem
Some clips are hard because the bats move fast and barely register. They're easy to follow while the video plays, but pause and step through frame by frame and they nearly disappear, each one a faint comet or streak of light instead of a clear shape. Your eye uses the motion to find them, and a single still doesn't give it much to work with.
Why it happens
A video frame captures a short exposure, a small slice of time. A bat that barely moves during that slice puts all of its light on one spot, so it looks bright and sharp. A bat that's moving spreads that same light along its path, so any one point is only a little brighter than the background. It's the streak a moving car leaves in a long-exposure photo. A fast bat is the extreme version, smeared into a faint comet. The faster it goes, the less it stands out in any single frame.
Fixing it comes with a trade-off. To pick up faint bats you turn detection sensitivity way up, and that also lets in more noise. You handle both sides by raising the sensitivity and increasing the speed setting (under Advanced) so ThruTracker allows targets that jump further between frames, then cleaning up the extra noise that higher sensitivity brings in.
Setting it up
- Load your video.
- Raise the detection sensitivity toward the "Maximum" end, and increase the speed setting under Advanced so faster, fainter bats still register.
- Set your core target settings for the clip: light or dark, number of bats (this workflow is for under about 20 per frame), and size. For size, match the width of the comet, the short way across the streak, not its length.
- Draw the gate somewhere with good contrast and little noise.
- Run a test and watch the result.
- If noise turns up, clean it with the exclusion filters (see False Detections). Re-run and adjust until it looks right.
Reflections Over Water
When this is your problem
When bats fly low over calm water, the surface mirrors them and you get close to double the detections you should: a real bat up top and its reflection on the water below, which ThruTracker can read as a second bat.
Why it happens
Calm water acts like a mirror.
Setting it up
Reflections give you two handles: where they sit (down on the water, below the bats) and how bright they are (usually dimmer than the real bat).
- Load your video.
- Mask the water. If the camera angle keeps the bats above the surface, paint over the water with the Exclusion Zone so its reflections are ignored. This only works when the bats and their reflections sit in different parts of the frame.
- Brightness, sometimes. Where the bats and reflections overlap, a brightness floor can drop the dimmer reflections while keeping the real bats. It only helps when the reflections are actually fainter, which is not always the case.
- Set your core target settings (light or dark, size, number of bats) and draw the gate above the waterline so only real bats count.
- Run a test and review.
Appendix: Project File Structure
When a project is created, ThruTracker generates a folder in the designated location containing the following subfolders:
- config — Contains the project's saved settings files.
- logs — Contains a history of runs and the settings used for each.
- outputs
- detections — Contains detection CSVs.
- figures — Contains graphics of emergence counts.
- overlay_videos — Contains processed gate count videos and any additional review video outputs.
- review_clips — Contains short review videos ~15s to be used for manually vetting counts.
- suspicious — Contains videos with unusually high activity that might be a person crossing the field of view or camera shake.
- review_images — Contains processed video review images.
- tracks — Contains track data CSVs.
The most frequently used files and folders are accessible directly within the application via buttons that open their respective locations after processing.
Roost Types
Every roost type has its own quirks. These sections work through them one at a time, split into the two places decisions get made: out in the field when you place the camera, and later in ThruTracker when you set the gate and detection settings. The same material, with walkthrough videos, is on the Roost & Species Guide.
Bat Boxes
What's unique
Bat boxes and multi-chamber "condos" are common across many species. Most have a single exit at the bottom, though some have several, and this guide is for boxes mounted on a pole; a box mounted flush against a building behaves more like the Buildings guide. Pole boxes are usually one of the cleaner setups: the camera looks up at the box against open sky, so bats stand out at high contrast, and the small, predictable exit concentrates the action in one part of the frame.
In the field
- Put the camera below or to the side, looking up at the bottom opening against open sky. That's your cleanest, highest-contrast background.
- A moving background creates false detections, especially rustling deciduous trees on a visible camera, so be mindful of the background when placing the box. A stationary background that contrasts with the bats is best.
- Frame the opening and the drop-out path with room around them. Don't let the exit sit right at the edge of the frame.
- Set the distance or zoom so a single bat is a reasonable size on screen, while still having sufficient buffer around the roost.
Analysis
- Gate: just below the opening, across the drop-out path, draw the gate sufficiently above the area where bats exit.
- Use exclusion size filters to ignore smaller free-flying bats in the distance.
Buildings
What's unique
Bats emerge from a large structure like a building or barn. You often don't know exactly where they'll come out, since a building has many possible gaps, vents, and eaves, and the exit may not be obvious until you watch an emergence. Contrast also varies a lot with the exit: a dark doorway or window, a sunlit exterior wall, and the building against the sky each look very different, so how well the bats stand out depends on where you film.
In the field
- Capture the whole likely exit area. Since you may not know the exact exit, frame broadly enough to catch wherever the bats come out, with the most uniform stretch of wall you can manage behind them.
Analysis
- Because the background changes with the exit, the bats may read lighter or darker than it, so set polarity to "Both" as a starting point.
- Because you don't know where the bats exit, draw a very large gate over the whole likely area and do a default run to find the activity (see Finding the action in long, low-activity recordings), then tighten the gate onto the real exit once you've spotted it. The run also produces a composite image of the tracks, showing all the movement at once, which makes the emergence points obvious.
Related guides. Finding the action in long, low-activity recordings.
Cave Entrances
What's unique
A cave or rock opening, usually filmed with the camera right up close, so the bats are large targets. They often circle for a while before they actually exit, so there's a lot of swirling action that makes manual counts really challenging.
In the field
- Get the whole exit in frame with a little room around it. Ideally the bats cross perpendicular to the camera, exiting left or right, with the entrance to one side of the frame and more room in the direction they travel.
- You can film a cave head-on, but it's more challenging: bats change size as they approach the camera, and their movement is radial, spreading in several directions at once.
- Favor a clean background. Bats stand out better against a clear stretch of rock than against foliage, and framing the entrance from below, looking up, can sometimes give an even cleaner backdrop.
Analysis
- Gate placement makes a big difference with caves. The rock entrance gives a gradient of contrast, so some areas are higher contrast and easier to detect than others, and bats bunch up, spread out, or swirl in different spots. Choose a spot where, in priority order: (1) contrast is high, (2) bats are spaced enough to read as individual targets, and (3) it is past the swirling range. Contrast and spacing matter more than clearing the swirl.
- Keep the gate off the frame edge, leaving a buffer at least big enough to detect a bat, so bats crossing there are seen on both sides and counted. The exception is when the frame does not capture the whole entrance and it runs off the edge; then some edge crossings are unavoidable and a few bats go uncounted.
- Looping bats are not a problem. If one crosses out and back in, it gets both an exit and an entry, so it cancels out of the net count.
Related guides. Zero or Negative Gate Counts (gate placement).
Trees
What's unique
Cavities, exfoliating bark, and snags. In most respects a tree roost films very much like a bat box: a small exit part-way up a trunk or limb, best captured from below against open sky. Two things make it harder. You often don't know exactly where the exit is until the emergence starts, and foliage works against you twice over, moving in the background and blocking the view of bats that have just dropped out.
In the field
- Start from the bat box setup: camera below or off to the side, looking up at the exit against open sky for the cleanest, highest-contrast background.
- If you aren't sure which cavity or crevice they're using, frame broadly enough to cover every candidate on that trunk, the same way you would with a building, then tighten up on later nights once you've seen where they actually come out.
- Work the sightline around the foliage. Leaves in the background move and generate false detections, and branches between the camera and the exit hide bats outright. Look for an angle that puts sky, not canopy, behind the drop-out path.
- Wind matters more here than at any other roost type, since a breeze sets the whole background moving. Film on the calmest nights you can.
- Expect only a short visible window. Bats often drop out and are into the canopy within a second, so place the camera to catch that first stretch below the exit and keep the gate close in.
- Be ready for more than one exit. A single tree can have several, and you may not know until the emergence starts, so film from more than one angle where you can, or bring a second camera.
Analysis
- Run a test over a section of the video before you commit to a gate. The run produces a composite image of the tracks, so the emergence shows up as a concentration of flight paths and you can see where the bats are really coming out (see Finding the action in long, low-activity recordings).
- Gate: just below the exit that test shows you, across the drop-out path, in the cleanest patch of sky you have, as with a bat box.
- Mask the moving foliage that isn't on the flight path. It is the main source of false detections at a tree roost, and masking it costs you nothing as long as the gate stays clear.
- Don't assume last night's framing and gate still apply. Tree-roosting bats switch roosts and exits readily, so recheck both each night.
Related guides. False detections (moving background), Finding the action in long, low-activity recordings.
Bridges
What's unique
Bridges are a hard one. Bats roost in crevices, expansion joints, and the spaces between girders, so a single structure can have exits spread along its whole length and bats leaving in more than one direction at once. On a big or complex site, complete coverage may simply not be possible. Mexican free-tailed bats are common bridge roosters, so a bridge colony can also be a very large emergence, with all the small, fast, overlapping targets that brings.
In the field
- Film the bats dropping down, with the camera placed below the bridge looking up at the cold underside if possible. That shaded concrete is the best background the site has to offer.
- If bats leave in a column, anticipate where that column will be and get as perpendicular to the bats as possible.
- If bats leave in multiple directions, you may need multiple cameras.
- Consider various placements to optimize for the background before you settle on one.
- On a complex site, focus on capturing the largest emergences, and note from concurrent visual observations to what extent the cameras captured the bats leaving. That note is what makes a partial count interpretable later.
Related guides. Very Large Emergences.
Very Large Emergences
What's unique
A very large emergence, where huge numbers pour out at once, typically at a large cave mouth or rock opening (Mexican free-tailed bat and Grey bat colonies). The camera is far from a big opening, so each bat is only a few pixels across, and a scene this large usually has varied contrast, so in some areas the small, faint bats are hard to pick out. The sheer numbers also crowd the frame with overlapping bats.
In the field
- For cave species, the framing is much the same as a cave entrance.
- You don't need the whole entrance, just a section where the bats are passing without overlapping too much, ideally against high contrast. If you've watched the emergence before, use what you know about where most of the flow is to pick that spot.
- Stay no further back than you have to; every extra bit of distance shrinks the already-small bats and makes them fainter.
- A higher-resolution camera helps here. With each bat only a few pixels, more resolution makes them easier to detect and to tell apart.
- A very stable camera matters here. The analysis is already challenging with such small, faint targets, and camera shake makes it worse.
Analysis
- Noise is hard to filter out here. The bats sit at the smallest end of the target-size range, so the exclusion size filter can't cleanly separate noise from real detections, and brightness exclusion is limited too since valid bats are faint.
- That leaves background subtraction as your main defense against noise, so keep it on where you can. Setting Max Density to Extreme (20+) turns background subtraction off to keep up with the heaviest activity, which can flood the frame with false detections, so use it only as a last resort, when the numbers are so high that nothing else works.
- Mask areas of swirling bats that aren't crossing the gate to lighten processing; only the bats crossing the gate need to be counted.
- You may need to increase the sensitivity to pick up the lower-contrast, fainter bats.
Species Profiles
What to expect from the species you are most likely to be counting, and how each one pushes the camera choice and the detection settings.
Mexican long-nosed bat
Leptonycteris nivalis · LENI
Roosts
Caves and abandoned mines, often vertical entrance shafts.
Cameras
Thermal Near-IR
In the field
- They emerge late, so visible cameras are not useful.
Analysis
- Likely need to use Variable Size Tracking with near-IR video, because changes in the wingbeat cycle can shift target size substantially.
Related guides. Cave entrance.
Brazilian free-tailed bat
Tadarida brasiliensis · TABR
Roosts
Caves, bridges, buildings, and bat condos. Colonies can be huge, 100,000s to millions, and they emerge before dark as a dense stream that can last several hours.
Cameras
Thermal Near-IR Visible
Push resolution and frame rate here. The emergence is huge, fast, and dense, and each bat can be only a few pixels, so higher resolution helps pick them apart and a higher frame rate keeps fast bats from streaking together.
In the field
- Frame the column for clean counts. Keep bats crossing perpendicular to the camera, picture where the gate will sit, and keep that zone free of clutter.
- A good vantage is often near the entrance looking out toward open sky: you get a clean backdrop and the bats move away from the camera, instead of filming the entrance head-on with bats coming toward you.
- Scout where the column tends to emerge, and how that might change with the weather. You may need multiple cameras to cover it.
Analysis
- A long emergence can span changing thermal and lighting conditions, so the scene may not look the same at the end as at the start. Plan for that when you set up.
- The biggest emergences may need Max Density at Extreme, which turns off background subtraction, so an empty, uncluttered background is especially useful.
- May need the higher speed option in Advanced settings.
Related guides. Caves, Very large emergences, Buildings, Bat boxes.
Gray bat
Myotis grisescens · MYGR
Roosts
Cave obligate in both summer and winter. The caves they use are cold, which gives strong thermal contrast and makes them easy to detect on thermal.
Cameras
Thermal
In the field
- Filming from inside the cave is sometimes an option, when there's a spot that's easier to film than the exit. They tend to fly near the ceiling, so a camera looking up can work well.
- Protect the camera from humidity transitions, especially when counting from inside a cave.
Analysis
- Very small targets, so select the smallest target size.
- Use masking for dense swirling areas.
Related guides. Very large emergences, Reflections over water, Cave entrance.
Myotis spp.
Various Myotis species · MYSP — including the Indiana bat (Myotis sodalis), little brown bat (M. lucifugus), and Yuma myotis (M. yumanensis).
Roosts
Mostly summer roosts in buildings and bat boxes.
Cameras
Thermal Near-IR Visible
These often trickle out of boxes and buildings only a few at a time, so you can get away with far less camera.
In the field
- Exits from buildings and trees can be unknown or shifting, so scout first and expect roost-switching.
Analysis
- Can be one of the most straightforward exits to count because they trickle out consecutively and don’t overlap much.
- Draw the gate sufficiently below the exit so each bat is counted both inside and outside the gate.