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Introduction to SonoBat and basic questions

[/heading][divider line_type=”No Line” custom_height=”4″][toggles accordion=”true”][toggle title=”Q: Is there an Owner\’s Manual for SonoBat?” color=”Default”]

A:Not yet, we are still working on it! But the other FAQs and Resources elsewhere on the site will answer many user questions. Also, there is contextual help built into SonoBat. To access this, simply locate your computer cursor on a feature in the SonoBat window and press CTRL-H (on a PC) or Command-SHIFT-H (on a Mac) and a pop-up window will appear with information about that feature. Moving your cursor to other features in the SonoBat window will dynamically change the information that displays in the pop-up window. For more information about all the features of SonoBat consider attending a Software Training Course or Field Workshop where students receive intensive training and hands-on use with SonoBat software and bat detector hardware for conducting acoustic surveys. For current information on available training see: http://www.batmanagement.com/Programs/programcentral.html

[/toggle][toggle title=”Q: What are the computer hardware requirements for running SonoBat?” color=”Default”]

A:SonoBat is available for both Windows and Mac platforms, and runs identically on either, plus recordings may be swapped seamlessly between the two.Windows Requirements: At Least Windows 7 operating system, Pentium processor with at least 2 GB of RAM, about 120 MB of free disk space (more will be needed as you collect calls), and a display 1024×786 pixels (xga) or larger.Macintosh Requirements: OS X operating system, Intel processor with at least 2 GB of RAM, and about 120 MB of free disk space (more will be needed as you collect calls).

[/toggle][toggle title=”Q: What types of bat detectors can record echolocation calls compatible with SonoBat?” color=”Default”]

A:In addition to the computer, a bat detector capable of recording time expansion sequences or direct-recording, full-spectrum triggered sequences is required. As a basic unit, we recommend the Pettersson D240x time-expansion unit, which has an auto-triggering function that will automatically retain and deliver 10x, time-expanded call sequences directly to a laptop or to a digital recording device and can be used for either active (e.g., voucher calls) or passive (unattended) deployments. Recorded calls can then be downloaded into the SonoBat program for processing and analysis. Other Pettersson units that work well with SonoBat include the D500x, D980x, D1000x and the M500. Specifications about these units are on the Pettersson web site (http://www.batsound.com). In addition, all Binary Acoustic Technology, Elekon, and Wildlife Acoustics full-spectrum, direct-recording detectors are compatible with SonoBat. To compare models and prices or to order equipment, see: http://www.batmanagement.com/Ordering/acoustic/hardware.html

[/toggle][toggle title=”Q: What USB Microphones work with SonoBat LIVE” color=”Default”]

A:SonoBatLIVE Works with all ultrasound microphones that show up under ‘input’ on your sound prefrences or Binary Acoustic Technology microphones. At this time the important one to note is that the Petterson M500 does not work on the mac version of SonoBat LIVE.

[/toggle][toggle title=”Q: How close does my detector microphone have to be to a bat to pick up a good-quality call sequence?” color=”Default”]

A:You can certainly detect most of the relatively loud tree-bats and free-tailed bats a couple of hundred feet away at least. Some lower intensity, whispering bats like the northern myotis, or Townsend\’s big eared bats, twenty feet (or less) is likely the maximum distance of detection. Moreover, lower frequency echolocation calls will travel farther in air before being attenuated, therefore bats with lower “characteristic frequencies” or Fc values will be more easily detected and will be detected at greater distances, than higher frequency bats. But in general, you need to be within about 100-feet to detect fully formed call pulses within a sequence.But, besides the intensity and frequency, another large part of the complicating factors involves the orientation of the bat toward the microphone. Bats emit their vocalizations with most of the energy directed forward. So the orientation of the bat relative to the microphone will profoundly affect the effective distance of perception. Just exactly where the bat is in the three-dimensional space in relation to the microphone will throw in additional stochasticity. So, if the bat is “off axis” to the best volume of detection of the microphone, calls will be increasingly difficult to record.Of course then there is a subjective assessment of “how good” of a bat pass do you need for confident chances of a species ID. Most biologists who determine occupancy based on acoustic recordings like to see about a dozen “fully formed” pulses in a sequence before rendering a confident decision. Fully-formed bat pulses including those that exhibit a harmonics in the recording and/or those with clear indications of low-intensity portions of the bat call present. Most of the passively recorded files you record will not meet these criteria.To increase the chances of recording high-quality bat passes, invest in a high-quality microphone. Independent testing amongst many biologists specializing in echolocation recording have identified the Pettersson D500x, particularly with the external microphone option, as one of the best detector/microphone combinations on the market today.

[/toggle][toggle title=”Q: What is the difference between SonoBat 3.2 and SonoBat 4?” color=”Default”]


[/toggle][toggle title=”Q: How reliable is the MLE calculation in SonoBat 3.2?” color=”Default”]

A:The Maximum Likelihood Estimates provide a probabilistic estimate and have no direct connection to certainty. The MLE calculation depends upon the absolute and relative counts of each species, and if there was a chance of their species count falling within the error rate of other classified species that sometimes get misclassified as those species. In other words, not a strong enough sample of a species\’ result for confident presence. (Of course that\’s the probabilistic result, but manual vetting could confirm or reject presence.) The standard MLE calculation is developed from a confusion matrix of classifier performance. However, such an approach uses idealized results from data used to generate a classifier. The SonoBat MLE calculation uses adjustments based on experience of classifier performance on real-world data sets.
When you interpret the SonoBat outputs, you should manually vet any files that come up as an unusual, unexpected, or one of only a few species at a site, manually check to see if it is a confident type of call sequence. (For more on confident type call sequences, see the Species ID FAQ section on this site.) The classifier operates by comparing the parameterized data from calls and how they fit into the parameter space of known species. Although SonoBat uses a number of redundant checks and attempts to recognize spurious signals and noise, some data still gets through that falls into some known data space and results in a misclassification. And of course that happens more often with files recorded under less than ideal conditions and/or with poor-quality equipment.

[/toggle][toggle title=”Q: What does the “corrected count“ mean in the SonoBatch-Summary file?” color=”Default”]

A:The Corrected count just considers the numbers of counts of each species and their known respective ambiguity from the classification matrix and decrements the counts for species that they might likely produce misclassifications accordingly to provide a more confident count. E.g., having a lot of Epfu counts will probabilistically generate some Lano, and an estimate of the number of Lano misclassifications that result from Epfu will subtract from the Lano count to make the “corrected count.” Even the corrected counts can still output misclassifications for difficult to discriminate call types. It\’s probably best to work from the Consensus decisions in the SonoBatch-Classify output (e.g., filter results by Consensus species, DP value (i.e., > 0.95), and #Files in the Majority decision (i.e., > 5)), and then manually vet these recordings to accept or reject enough files to confirm presence or absence of a species.

[/toggle][toggle title=”Q: I noticed that there isn\’t a regional classifier for my area. Can I use one that has more species than I need and “turn off“ the ones not in my area, before running the auto-classifier so I can get a more accurate result?” color=”Default”]

A:No. The sophisticated classification algorithms SonoBat uses does not allow for user-inputs. It is best to use the classifier for your region and then manually vet results for species that do not occur in your area, with the understanding that misclassifications may result among the classified species. Check the SonoBat website frequently as we are constantly developing new and improved classifiers and adding regional species sets.

[/toggle][toggle title=”Q: Can I add reference calls from my personal voucher call library to the SonoBat 3.2 automatic classifier?” color=”Default”]

A:No, but you can submit your reference calls to us for consideration as we continue to improve the SonoBat regional classifiers. For submission instructions see My Account.

[/toggle][toggle title=”Q: What are SonoBat Utilities and why do I need them?” color=”Default”]

A:The SonoBat Utilities include several helpful programs for post-processing large batches of recordings from any type of full-spectrum detector, an auto-recorder for making unattended recordings, and a reference compiler to create “reference views” from your personal bat call library. For more information about each of these programs and tips for their use, consult the information in the SonoBat Utilities FAQ section on this site.

[/toggle][toggle title=”Q: What is the bright green graphic under each spectrograph?” color=”Default”]

A:That is the oscillographic representation of the bat call. This is the high frequency sound wave-form, illustrating how the intensity (amplitude) of the wave changes over time. When the green lines fill the window top to bottom, the sound is at its most intense (loudest). When the green lines are aligned with the midline in the window the sound is at its least intense (quietest). This corresponds with the color intensity representation of each call pulse in the main SonoBat window. Quieter, less intense, portions of the call are rendered in blue and as the call becomes louder the color changes from green to yellow to orange to red, representing the most intense (loudest) portions of the call.

[/toggle][toggle title=”Q: What is the difference between “real-time“ and “compressed“ view and when should I use them?” color=”Default”]

A:Compressed view will expand call pulses into the silent periods in-between pulses, this allows users to see more of the nuance of call shape and perform qualitative analysis to determine species identification. In compressed view, all information about the relative time between call pulses is lost and the call pulses are displayed evenly across time.Real-time view preserves all information about the relative time between call pulses and makes it easier to identify approach-phase or acquisition-phase call sequences (e.g., feeding buzzes). It also allows users to better identify when two bats of the same species are captured in a single recording.

[/toggle][toggle title=”Q: How do I compare my recordings with known species from a call library?” color=”Default”]

From either view, a single pulse can be selected by using your cursor to draw a box around the pulse, then that pulse can be displayed at a “standard view” magnification. In this mode you can “Enable Analysis” to show select call characteristic metrics, write those metrics to a *.txt file, or “append a reference view” so it can be compared to the library of voucher calls which came with the software. The “Reference View Compiler” utility will allow users to create their own reference views and add them to the SonoBat reference view library. See more information on using the Reference View Compiler in the Resource section of this website.

[/toggle][toggle title=”Q: When I click “Append Reference View“ why is the open file dialog box empty?” color=”Default”]

A:SonoBat must first be set up with a “default reference view” path. To do this, click on the “set prefs” button in the lower right hand corner of the SonoBat window to pull up the SonoBat Preferences dialog. Select “click to brows to directory” and locate the appropriate ref views folder (i.e., either “eastern US ref views” or “western US ref views”) in your SonoBat Program File location. To accept this designation, click the green “Save” button in the lower right hand corner of the pane or press Enter/Return on your keyboard. Now when you select “append reference view” in your SonoBat window, the dialog box will contain the entire reference view library. Species are listed in alphabetical order by scientific name, and the “up” and “down” buttons to the right of the “append reference view” button will allow you to page thru the collection in order, without having to “open” each file. Reference views that are made up of compilations of single pulses from each species, illustrating that species\’ repertoire have an underscore (“_”) prefix, individual single pulse reference views have no prefix.

[/toggle][toggle title=”Q: When I analyze a call and exported data to a file, the field “PrecedingInterval“ is regularly set to zero.The field “CallsPerSec“ is improper too. What have I done wrong?” color=”Default”]

A:Perhaps you may be attempting to extract call data in realtime mode. SonoBat only calculates call intervals when it performs call discrimination to display in compressed view mode. In realtime mode, call parameterization will always output a zero for PrecedingInterval for that reason.The “mean calls per second” displays the value for the mean calls per second of the recording or the section of the recording displayed. The accuracy of the reported value depends both on the quality of the recording and the absence of other bats in the recording. Any other signal components other than the bat of interest that pass thorough the discrimination logic will be counted as calls and contribute to (and reduce the accuracy of) the calculation.

[/toggle][toggle title=”Q: How do I change the filename of a recording?” color=”Default”]

A:Simply place your cursor in the filename box a the top of the main SonoBat window and click. You can change all or part of a name or pre-pend or append the existing file name simply by typing text into this box. When you are satisfied with the edits to the file-name, click the “chng” button above and to the right of the filename box, otherwise your edits to the filename will not be saved. Consider adding text to the end of the file name in order to preserve the sort-order of your files. Add text to the beginning of the file name to help sort out unwanted files (e.g., feeding buzzes or approach phase calls that have little chance of confident species ID determinations).

[/toggle][toggle title=”Q: How do I change the meta-data associated with a recording?” color=”Default”]

A:In “standard view” click the “edit file attributes” button on the lower left side of the main SonoBat window. An “edit file note” dialog box will appear and information can be added, deleted, or changed simply by typing in the large gray box at the top of the window. Press the “save” button or Return/Enter to execute the change. To change the meta-data associated with an entire folder of files, see the information about the Batch Attributors in the Utilities FAQ section of this website, or in the Utilities section of the Resources.

[/toggle][toggle title=”Q: Can I listen to the bat calls in a *.wavfile?” color=”Default”]

A:Make sure your volume is adjusted on your computer then click either the “play real sound” or “play TE sound” buttons in the top right corner of the main SonoBat window. The real sound will produce a realtime series of clicks similar to the output on a heterodyne or frequency-division bat detector. The TE sound will produce a time-expanded version of the bat call, slowing down the recording by a factor of 10 and allowing the user to discern more nuance about the pitch of each bat call pulse. A fine red vertical line will be displayed in the oscillogram window and keep pace with the audio output so listeners can follow along with which call pulses are associated with the audio output.

[/toggle][toggle title=”Q: How do the “filters“ in SonoBat work? What\’s the difference between a 10kHz filter and a 10kHz cut-off filter?” color=”Default”]

A:First, do not confuse the term “filter” as used by SonoBat as anything at all like the term “filter” as used by Anabat. SonoBat uses the term in the more generally interpreted sense in signal processing. i.e., selection and elimination of specific frequency bands.
SonoBat displays the full-spectrum sound files in two dimensions simultaneously, the time-frequency domain with frequency on the x-axis and time on the y-axis, and the time-intensity domain, as indicated by the “color-weather radar” pattern in the call pulses represented by how the amplitude of the wave form changes with time in the green oscillographic representation below the call sequence along the same time-scale. The time-intensity representation is displayed relative to the loudest sound in the file. If there is another low-frequency (e.g., 5-20kHz) ultrasonic sound source, either biological or anthropogenic, which is significantly louder than the bat call, it can mask the relatively quiet, higher frequency (e.g., 20-90kHz) bat echolocation sequence. Filters are used to reduce or eliminate the interloping low-frequency noise so the time-intensity domain of the bat call can be emphasized.
The 5kHz filter is the default setting. It eliminates most sounds below 5kHz which often carry just interfering environmental noise and no components of bat calls. For higher frequency bats ( 40kHz and above) the 10, 20, 25 or 30kHz filters may be useful. The “cut-off” and “anti-katydid” filters apply a more powerful attenuation of signal information below their designated frequencies, but may also introduce some artifacts on the existing signal information from this processing.
Consider the SonoBat auto-filter like an automatic transmission on your car: It will do a reasonably good job by itself, but for real performance driving you want the full control of a manual transmission and clutch. That said, if you know you have no species below 20 kHz, then just run a manual 20 kHz cut-off (or anti-katydid) filter, and eliminate anything below that frequency, and this will emphasize everything above that frequency, i.e., the bat calls.

[/toggle][toggle title=”Q: How do I create a zoomed section of a bat call and why would I want to?” color=”Default”]

A:you can save a “zoomed” section of a recording, making one or more shorter sections of a longer recording. You might want to do this for various reasons: (1) You can make two 8-second zoomed sections of a longer 16-second recording, (2) You can eliminate unwanted noise at the beginning or end of a file so that the intensity of the bat echolocation call pulses (e.g., non-noise sound) is rendered more faithfully, or (3) You can make separate files out of sequential bat passes from two different bats or two different species in a recording. To do any of this, make sure the “real-time” viewing option is active, then open the long recording, use your cursor to move the fine yellow vertical bar to select the first half of the recording in the oscillogram view. Use your cursor to draw a box around the call pulses displayed in the main SonoBat window, then press the “save zoomed section” button. A dialog box will open showing you the new name of the file for the zoomed section allowing you to re-name the zoomed section before saving. E.g., the file name will be your original file name with “-zoom” appended. Note unless one or the other of the zoomed sections are renamed something different, the second zoomed section will overwrite the first. To prevent this, add an “a,” “b,” and/or “c” etc., after the original file name for each zoomed section created from a single file. This allows the original file to appear before any zoomed sections in the file list when sorted alphabetically.

[/toggle][toggle title=”Q: I still have more questions about SonoBat basic operations, where can I go for answers?” color=”Default”]

A:The other FAQs and Resources elsewhere on the site will answer many user questions. Also, there is contextual help built into SonoBat. To access this, simply locate your computer cursor on a feature in the SonoBat window and press CTRL-H (on a PC) or Command-SHIFT-H (on a Mac) and a pop-up window will appear with information about that feature. Moving your cursor to other features in the SonoBat window will dynamically change the information that displays in the pop-up window. For more information about all the features of SonoBat consider attending a Software Training Course or Field Workshop where students receive intensive training and hands-on use with both SonoBat software and bat detector hardware for conducting acoustic surveys. Information about the current course offerings can be found on at this link:

[/toggle][toggle title=”Q: I don\’t think features on my SonoBat software are working as described, where can I go for support?” color=”Default”]

A: Please contact info@sonobat.com for more information.