This is a first version of the Manual for BatScope 3 ! We can improve the manual with your feedback: BatScope email ! Please mind, that many items (colored text) in this document are linked to other sections for cross reference.

Feature Overview

With BatScope, you can

  • transfer your BatLogger (and other) recordings from SD card to a well-structured database on your Mac.
  • easily browse your collection of bat recordings and get an overview over their contents.
  • view spectrograms of recorded sequences.
  • cut recorded sequences into single bat calls.
  • automatically analyze and classify bat calls to species, using different classification systems. Restrictions apply, see the Judging and Improving Classification Quality section below!
  • track your route of recording via BatLogger GPS records comfortably in Google Earth.
  • search, filter and sort your database of bat recordings by any criteria such as time or location.
  • export the results, classifications or whole sounds and easily share with other users.

System requirements

  • Mac OS X 10.6 (Snow Leopard) or newer
  • 1 GB RAM (2 GB recommended), 1 GHz CPU
  • SD card reader for importing from BatLogger SD cards directly
  • considerable amounts of available disk space, for storing large projects with many recordings
  • Google Earth and Raven (Pro or Lite) are recommended for full exploitation of all features

Technical Information and Installation

BatScope is bundled in a single installer file. By installing BatScope the following packages will also be installed: Batit, Python 2.7 and wxPython for Cocoa.

The BatScope installer places the file in /Applications/BatScope. This file is a bundle that not only consists of the BatScope application but also all related database files. The old file will be renamed You can place BatScope anywhere on your filesystem and also make copies, either as backup or to use them as different database to additionally structure your data. Because the consists already of all program data, you can have different copies of BatScopes on your filesystem. However, it is not recommended to open more than one at the same time.


If you are working on many topics containing different projects, you may use different copies of BatScope, which, for better reference, you can also uniquely rename (BatScope_UVP, BatScope_Migration, etc.). The name will show up in BatScope‘s main window. Copies may help you to keep data better organized.

See Updating to a Newer Version of BatScope below for an explanation how to move data from an older file to a newer one.

The BatScope database is a mere structured mapping of imported data and as such does not contain the raw recordings or classification results itself. Instead, all images, audio files, etc. are stored on disk, outside of BatScope files, in project folders, and are only referenced in the database file. This allows BatScope to handle thousands of audio recordings, of which the raw data can use many gigabytes on disk. All important information contained within the database is consistently stored on disk, so losing the database doesn’t equal loss of data. You can reintegrate existing data from disk into a database at any time, see the Moving, Deleting and Reimporting Data section below.

BatScope is built with and around a FileMaker© runtime database. Therefore the usual database operations like searching and sorting also apply to BatScope.

See Uninstalling below for guiding through uninstalling BatScope.

Getting Started

First Steps

Start BatScope by executing located at /Applications/BatScope. You will see a splash screen asking for registration. Registering your copy of BatScope is free; a registration key will be sent to you by e-mail. Aside from the splash screen, no limitations apply to unregistered versions of BatScope. Your registration information will only be used to inform about future versions of the software.

The BatScope database is organized in four hierarchy levels, allowing you to organize your data in a well-structured way. These are: projects, SD cards, sequences, and calls.

Create your First Project

welcome screen

Figure 1: The first startup screen.

After the splash screen, a Welcome layout will reveal itself. Select Create a new project button on top. The path you’re then prompted to specify determines the location where the project folder will be created. You can specify the project title and an author for each project. A new empty project panel with the name you specified will then appear in the Overview layout.


Mind the interactive texts and elements that appear all over most layouts! The cursor changes to a little hand over these active elements, and after a short while a little Pop-up Help will give some tool tips about the element’s functionality. Explore!

Import Data from a SD Card

Insert an SD card containing recordings from a BatLogger into your Mac, or have a folder containing data ready. Click the New button in the project panel and select the path to the SD card or the aforementioned folder in your file system. You can now see your SD card listed. If a folder contains multiple SD cards, all will be found and listed. You can exclude SD cards or edit the SD card’s names in the list. Click on Import listed SD cards. The contents of the original SD card are left unchanged.


We differentiate between importing new data from recording devices and integrating data already imported previously, e.g. with an earlier version of BatScope or in the framework of another project (e.g. exchanges).

Cutting and Classifying Sequences

Clicking on the name of the imported SD card will switch you to the Sequence List layout, showing the sequences contained. Select some sequences by clicking the grey quadratic checkbox.
green circle

Figure 2: Available processes for sequences.

On the top under Process choose Cut and classify and click go and confirm the dialog that warns of potentially overwriting already cut calls. The selected sequences will now be cut into calls and classified. Afterwards, by clicking on the number of calls you can view the found calls of a sequence in the Call List layout. Klicking on a spectrogram image will display the Single Sequence layout, that gives more details about the recorded sequence.

Moving, Deleting and Reimporting Data

Moving a Project

The file stores references to physical files in the project folder on disk, such as audio files or spectrogram images. If you wish to relocate a project folder to a different location, because you’re running out of disk space for instance, click the Move button in the project panel in BatScope, select Select Path and choose a new directory. After you confirm with Move, BatScope moves the physical files to the new location and updates the database accordingly.


A project folder may use many gigabytes of disk space, depending on the number of audio sequences and bat calls it contains. Moving may thus take a long time to complete, e.g. when moving projects across different storage devices, such as external hard disks.

You can also move your project folders manually in the Finder and later press the Edit button in the project layout to update its path. BatScope will recognize that the files have been moved and prompt you for the new path.

Moving SD Cards to a Different Project

Projects can only be moved in whole. If you just want to assign an SD card to a different project, do so via the Move button near the SD card entry in the project panel. This also relocates the SD card folder on disk from the source project folder to the target one for you. Be aware: moving SD cards may take a considerable time, as the content of many files on disk have to be updated and rewritten. (This operation should be accelerated in an upcoming revision).


Single audio sequences cannot be reassigned to a different SD card.

Deleting Projects and SD Cards

In BatScope you can delete projects and SD cards by clicking the corresponding red Delete button in some layouts. Whenever you click a Delete button, you’re asked whether to only delete the corresponding record in the BatScope database and leave the physical files on disk untouched, or remove both. In the first case you will later on be able to restore the deleted project or SD card, because all relevant information in the BatScope database is always consistently written to the physical files it links to. In the second case the data will be erased from the database AND the physical files will be erased from disk. There is no undoing to this operation!

Reintegrating Data

As stated under Import data we differentiate between importing and integrating data, the latter meaning integrating data previously removed from the BatScope database. This can be achieved from the Overview layout. You may either integrate a set of project folders, for each of which a new project will be created in the database, by clicking the Integrate project folders button on top, or integrate a set of SD card folders, for each of which a new SD card record will be added to a chosen project, by clicking the Integrate button in a project panel. Either way, all contents of what you selected will be reintegrated recursively. This allows you to restore multiple projects with many contained SD cards all at once, with just a few clicks. Reintegrating can take time for large amounts of data. Just like during initial import, you are shown what is currently being reimported in the process, and the whole integration process can be aborted by clicking the corresponding button on the bottom.

Sharing Data with Others

This technique of integrating offers an easy way to share your data with others. Make sure that BatScope is closed when copying any data folders to ensure all modifications have been written to the filesystem. Then simply pass a copy of one or multiple project folders and/or SD card folders along. The recipient will be able to integrate them into his BatScope database precisely as described above. Make sure you have full read and write permission for all data to be reinegrated, especially when sharing projects with other users. You may have to run a chown or chmod command in Terminal on the folders before reimporting data from other users.

Exporting data from within BatScope offers another option to share data. For details see Exporting Data.

Classifying Bat Calls

From the Sequence List layout, any number of audio sequences can be selected and processed all at once. For instance, you may click an SD card from a project panel to see all imported audio sequences from that SD card in the Sequence List, select them all by clicking the All button on top, choose Cut and classify from the process pop-up menu, and hit Go. This will launch a subroutine which cuts out the detected bat calls from the sequences and classifies them using all built-in classifiers. You will see a pop-up window showing progress information in the process. Analyzing and classifying audio sequences is an I/O-intensive and CPU-intensive task when performed on a large number of recordings. The process will make use of all available CPU-cores, thus your progress window might show several processing threads. It still may take a long time to complete, and it may produce gigabytes of data if the selection of sequences is in the thousands.


Only the displayed and selected sequences are processed; sequences that may be selected, but which aren’t contained in the current found set, i.e. which are not shown, are not included in the process. Classification is possible only for sequences in whole, not for single calls.

Three classifiers are implemented: The Support Vector Machine (SVM_), a K Nearest Neighbor (KNN_) classifier, and the standard Quadratic Discriminant Analysis (QDA_). You may classify any sequence with only one of the classifiers by selecting the corresponding entry in the process pop-up menu in the Sequence List. The general Cut and classify and Classify items include all three classifiers. More information about classification is found under Classification Background below.

Judging and Improving Classification Quality

Confidence Interval Tests

After each classification, i.e. each time a classifier has proposed a most likely species for a call, the three most distinctive features of the call are tested against stored reference values of that proposed species. These features are: Call duration, peak frequency and bandwidth. If any of these values lies outside a 95% confidence interval of the training set’s average of the proposed species, the confidence interval tests (CIT) are marked with Fail in BatScope, indicating a questionable classification result. Otherwise a Pass indicates the values to be within the 95% confidence limit.

BatLogger Settings

For best usability within BatScope, we recommend to restrict the maximum sequence duration to approx. 10 to 20 seconds on your BatLogger device. You can achieve that by editing the setup file BATPARS.xml on the SD-card of your BatLogger with the help of either the dedicated editor (BATPARS Editor) or with a plain text editor. Change <AUTOTRIG_MAXTIME_MS> 53500 </AUTOTRIG_MAXTIME_MS> to <AUTOTRIG_MAXTIME_MS> 15000 </AUTOTRIG_MAXTIME_MS>).

The longer the recording, the bigger the chance to potentially contain hundreds of bat calls, which increases the chance of getting ambiguous classification results in BatScope. As classification statistics are always gathered by calculating over whole audio sequences, longer recordings also increase the chance to record two or more bats simultaneously, thereby further complicating the assessment in the end. On the other hand, from a passing bat the recording of 15 seconds still allows to collect a statistically meaningful sample of echolocation calls for analysis.

Verifying Sequences

BatScope calculates species attribution of recordings by multiple classification of the contained echolocation calls, and subsequent summary statistics of all calls activated in the sequence (See Call List layout for detailes on de/activating calls!). Take this attribution as an educated proposal of what the real species might have been recorded. This is not the final species attribution, that BatScope will store and export, but it deserves the operators verification, read control and consent, of the proposed species. For some species, e.g. Pipistrellus pipistrellus, this will be a straight forward process, for others, e.g. Myotis brandtii the process might take time, iterations and quite likely acoustic comparison with other recordings (the free WSL software BatEcho offers such possibilities). Potentially the verification even deserves prudent classification to a higher taxonomic level, e.g. species-complex, genus or even genus-complex.


Never accept BatScope classifications blindly. We stress the notion, that there are many pitfalls in any classification procedure, and that verification is compulsory before working with a species list!

BatScope gives you the option to verify or edit classification results on a per sequence basis. There are two different approaches. If you verify or edit a set of selected sequences, that you are certain about the classification, these will become Automatically Verified. On the other hand, if you work with single sequences, these will become Manually Verified. This differentiation exists to keep you informed about which sequences you examined more closely (Manually Verified) and which you only examined as a group (Automatically Verified).


Figure 4: Possible options for verifying sequences.

  • Automatically Verify: Assuming you have a set of selected sequences, you can use the verify options under Process in the Sequence List layout.


    If you do not automatically verify all species proposed by the automatic classification process (marked initially with AC), the classification will become marked as manual or MC.


Figure 5: Options for overriding automatic classification.

  • Manually Verify: You can either use the Single Sequence or the Single Sequence Large layout and use the various buttons under Verification or the shortcuts listed under Shortcuts - Arrow Classification. The advantage of the shortcut method is that you can use it from every layout except the overview.


    If you change the call basis of a sequence by deactivating or deleting calls, its verification becomes outdated. The exact behavior is described in Outdated Sequence Calculation Data.

Updating to a Newer Version of BatScope

Updating from BatScope 2.x to BatScope 3.x:

Select Integrate project folders in the Overview layout. You can now select your BatScope 2 projects which will then be integrated into BatScope 3. Depending on the amount of data, this may take some time, as BatScope 3 creates additional data structures (a SQLite data base)!


If you want to continue to use BatScope 2 you must work on a separate copy of your project files. It is not possible to consistently use your project files in BatScope 2 anymore once you have integrated them into BatScope 3, because the new version makes use of additional data structures.

Updating from BatScope 3.x to a newer version

Open an new empty BatScope database and select Import Database from the File Menu. Select your old BatScope database (application) file and all records will be imported in the new database. The old BatScope database will not be modified and remains fully functional.

This is by far quickest way to update to higher versions of BatScope 3. However, you still can integrate old projects as described above.


BatScope does not need any uninstalling. Because the BatScope application file contains all program and database data you can just remove this BatScope application file.

The BatScope installer also installs Batit into the applications folder and an accompagnying framework /Library/Frameworks/BatitSnd.framework that you may want to remove if completely uninstalling. Python 2.7, and wxPython for Cocoa are additionally installed. Due to varying dependencies please refer to the documentation of these packages for instruction on how to uninstall them.

Advanced Topics

Enabling and Disabling Sequences and Calls

In the following, we describe features that help you to organize your sequences and calls, thereby also improving the statistics. You can exclude data from your workflow without deleting it, but you can also delete it from your filesystem if you are sure that you don’t need it anymore. To that purpose, we added states to sequences and calls. Each sequence and each call can have three states: Enabled, Disabled, or Marked to Delete.

Sequence states


Figure 6: In the Single Sequence layout large buttons at the top allow changing the selection, activation and deletion states.


Figure 7: In the Sequence List layout small buttons at the right of the spectrogram allow changing the selection, activation and deletion states.

  • Enabled and Disabled: This states exist solely to help you organize your data. For example, you can disable all sequences you are currently not interested in and filter only for enabled ones. All sequences are enabled by default.


    When verifying, a first species of several verified in a sequences already marks the corresponding sequence as verified! You can use the feature of enabling / disabling e.g. to keep sequences enabled, until you have made sure that all contained species are verified. Only disabled sequences would thus mark all your finally processed sequences.

  • Marked to Delete: If you don’t need a sequence anymore you can mark it for deletion. This will also disable the sequence. All sequences marked for deletion can be deleted at once from the disk by selecting Delete Sequences Marked for Deletion in the Preferences layout. You can revert the Mark to Delete-tag at any time as long as you have not really deleted the sequences through the preferences layout. Also, closing BatScope will not delete any sequences.

Call states


Figure 8: In the Single Call layout large buttons at the top allow changing the selection, activation and deletion states.


Figure 9: In the Call List layout small buttons at the right of the spectrogram allow changing the selection, activation and deletion states.

  • Enabled: The classification data of the call will be included in the sequence calculations. All calls are enabled by default.

  • Disabled: The classification data of this call will be ignored for the calculation of the summary statistics of species contained in a sequence. Typical indications for disabling calls would be:

    • the quality of the classification is low
    • parameters don’t fit (CI test failed)
    • classifiers do not agree on the identification
  • Marked to Delete: If you don’t need a call anymore you can mark it for deletion. This will also disable the call. All calls marked for deletion can be deleted at once from the disk by selecting Delete Calls Marked for Deletion in the Preferences layout. You can revert the Mark to Delete-tag at any time again as long as you have not really deleted them using the preferences layout. Also, closing BatScope will not delete any calls.

    Deletions are not elicited immediately for performance reasons. For further information see the Preferences layout, from where actual deletion has to be triggered.

    If you change the status of a call the calculation data of the corresponding sequence will become outdated, which will be explained in more detail in the next section.


You can delete calls and sequences marked for deletion in the Preferences layout. There you can also select if you want to only move the data to the trash or to delete it directly. The former works much more quickly and allows the user to remove the data asynchronously by emptying the trash in the finder later.


For reasons of data consistency between database and filesystem, it is not possible anymore to delete a sequence or a call from the database only (as it was possible in BatScope 2.0). This functionality is now effectively achieved by disabling sequences or calls.

Outdated Sequence Calculation Data

For performance reasons, when you change the state of a call, the calculated data of the affected sequence will not be recalculated immediately. As you potentially work on thousands of calls in hundreds of sequences, the updating may take considerable time. Instead, all affected data that need to be recalculated will be marked red.

Figure 10: When disabling calls, the corresponding sequences momentarily indicate outdated statistics with red color in the Call List and Sequence List layouts and the Calculate and Save button becomes highlighted red.

Press the Calculate and Save button to recalculate. After execution, you will notice that the calculation data of all sequences will turn white again.

Verification Outdated

By changing the activation state of calls of a sequence, verifications (automatic or manual) might become invalid or outdated. Therefore, if a sequence was manually verified, it will become outdated manually verified, and if it was automatically verified it will become outdated automatically verified as soon as you change the status of an associated call, and the corresponding marks AV or MV become red in these cases.

Figure 11: The highlighted mark for the verification (AV or MV) becomes red when the call basis has changed in a previously already verified sequence. For a detailed description of the abbreviations see Sequence List layout.

You have several options to reverify your sequences:


You can change a set of selected sequences to automatically verified using the following processes in the Sequence List layout:
  • Reverify auto.: This processes sets all selected sequences with the verification status outdated automatically verified to automatically verified again.

  • Reverify all: This processes sets all selected sequences with the verification status outdated automatically verified or outdated manually verified to automatically verified.

    In the Single Sequence layout you may use Reverify to set any.

Reverifying from the Single Sequence Layout

You can change a sequence to manually verified by either accepting or manually selecting a species. If a sequence is already verified (this includes outdated and automatic verifications) you can set it to manually verified by pressing Reverify.

Figure 12: The Reverify button in the Single Sequence layout changes verification in a Outdated Manually verified sequence.

Exporting Data

From the Process drop-down list in the Sequence List and the Call List layout you have various options to export data. The summary data (Spreadsheets) will be exported in the folder you provide in the dialog. Exporting sequence or call data will rebuild the data structure of your projects in the folder of your choice. This also includes the text file Information.txt, which is compulsory for reintegrating the date into another BatScope, e.g. after exchange with another user.

Figure 13: Export options from the process menu in the Sequence List layout.

Exporting Sequence Data

  • Export to Excel: Exports the numeric data of selected sequences into an Excel sheet. For every record in BatScope you get a line in the exported Excel sheet.

  • Export Sequences: Copies all sequence data, the .batseq files of the selected sequences, to the specified folder.

  • Export Seq./Calls: Additionally to the above, this copies also all associated calls, the .batcall files, to the specified folder. The -.batseq_Calls folder will furthermore contain a file calls.txt, which contains all measured parameters of the calls in the respective calls folder.

  • Export .wav Files: Copies only the pure .wav files of the selected sequences to the specified folder.

  • Export Class.: Exports an Excel file with all sequence data such that every end classification will be placed on a separate row, thus exporting as many rows as species have been verified, potentially more than sequences selected for the export! This is extremely useful for sequences, that contain more than one species.


    Sequences which are NOT verified will not be exported!

Exporting Call Data

  • Export to Excel: Exports the numeric call data of selected sequences into an excel sheet.

  • Export Sequences: Copies the call data, the .batcall files of the selected calls to the specified folder.


    Please use an HFS+ formatted (not FAT, NTFS or other) disk for sharing files, to guarantee all Mac file information can be written to and is pertained on the disk.

Classification Background

All classifiers have been trained and optimized on a training set consisting of 19’672 recorded calls of 27 Swiss bat species. The underlying feature set, consisting of 23 features per bat call, is the same for all classifiers. It includes the frequencies and slopes of the call trajectory, the call duration, the peak frequency, percentiles of the energy distribution and other differentiating features. The three classifiers perform differently on this training set and are expected to differ also in their ability to correctly recognize new bat calls (different generalization performance). To provide some intuition of how trustworthy the results of each classifier are, and to help you with identifying wrong classification results, the cross-validated generalization performance of each classifier is tabulated in Table 1 below.

Classifier Percentage
SVM 86.5 %
KNN 84.9 %
QDA 81.1 %
Agreement rate 76.4 %
Correct if agreeing 95.7 %

Table 1: Cross-validated sensitivity of the 27 trained species for each classifier separately and under the condition that they all agree on the species.

Table 1 shows the true-positive classification rate (“sensitivity”) within the mentioned training set obtained from 10-fold cross-validation, averaged over all training data. The most reliable classifier is SVM, with an average sensitivity score of 86.5%. The fraction of classifications where all three classifiers predict the same species is 76.4% on average over all species, and when they do agree, the prediction is correct with very high probability (95.7% on average).

Since these values are obtained from 10-fold cross-validation, but the classifiers implemented in BatScope are trained on all available data, the actual prediction quality is slightly higher than the values tabulated.

Classification Statistics

The Classification Statistics layout, which is accessible for each sequence from the Single Sequence layout through the Details button, provides helpful insight into the results of the automated classification.

Figure 14: Summary statistics details over all activated calls of the sequence in focus; view is accessible from the Single Sequence layout.

The assignment of single calls to bat species is summarized within a single sequence, and a few statistical key values are tabulated. These data can help you with verifying the correctness of the automated classification, and with identifying wrong classification results.

Each classifier, when given a call, returns a confidence or probability estimate for each species indicating how likely the call originates from that species. Based on the highest two confidence values (1st and 2nd guess) for each classifier and each call within a sequence, the following statistics are calculated:


  • Absolute: The number of times within the present sequence a species was automatically identified as the most likely species of a call. The most likely species is that with the highest classification confidence when summed over all classifiers and both ranks (best and second best guess).

  • Relative: The same, but as percentage of the total number of calls, i.e. multiplied by 100% divided by no. of calls.

    Most often, a single recorded sequence captures no more than 1-3 different bat species flying by. Thus, species which are less frequent than the highest ranked 1-3 species are likely to have been misidentified by the automated classifiers. Often, you will see a clear drop in frequency after the first or second most frequent species.


    This is a rule of thumb, not a certified measure.


  • As 1st: The average confidence a species acquired from all classifiers as the best guess within this sequence. Species with a high confidence as 1st are more likely to be effectively present than others. A species that is in fact absent from a sequence may in principle still obtain a fair share of probability by the classifiers, e.g. if many of them rank it in second place. Such species will have a low confidence as 1st, because that value only considers likelihoods from each classifier’s best guess per call.

  • Normalized: The total sum of confidence a species has acquired from all classifiers (1st and 2nd guesses) within the present sequence, relative to the other species, independent of the number of votes the species got. These values do not quite add up to 100% over all species and within each sequence, because ranks lower than 2nd are not considered. 100% corresponds to the total sum of all confidence values from all classifiers and for all calls within the sequence.

  • Species: The average confidence per vote (1st or 2nd from any classifier) a species has acquired for calls within the present sequence. Unlike the normalized confidence, which compares the sum of confidences among the species, this value indicates how sure the classifiers are when proposing the species as one of the best two. In other words, it takes the number of votes that lead to the sum of confidence into account.

  • CIT Success: (Confidence Interval Test) The fraction of calls assigned to a species that passed all three confidence boundary tests for all classifiers (see previous section Judging and Improving Classification Quality). A high CIT success rate doesn’t necessarily signify a correct classification, but a low rate often points at poor classification results.


    The confidence values give additional information to judge correctness of a classification. Use also spectrogram views, compare measured parameters to literature and comparatively listen to reference calls of known species.


  • 1st: The number of times a species has been proposed to be the most likely species by one of the automated classifiers.

  • 2nd: The number of times a species has been proposed to be the second most likely species by one of the automated classifiers.

  • Total: The sum of the two above, i.e. the number of votes a species obtained from the classifiers for the present sequence.


    The number of votes is not normalized by the number of classifiers. Sequences that have been classified with two classifiers will get more votes in total than ones with only one classifier. The number of votes thus cannot be used to compare sequences, only to compare species within a sequence.

    The button Go back will bring you back to wherever you triggered this layout from.

Converting and Importing Foreign Audio Data

A software called BatImporter is integrated into BatScope. It allows you to import data (SD cards) that are not generated by the BatLogger. You can open it by pressing Convert in the Overview layout. After selecting your device from the list you can import SD cards or data folders as if they were recorded with a BatLogger.

The Show Details button (Figure 16) will help you choose the right converter type for your data. Presently BatCorder first and second generation and Pettersson D500X include generic meta file import.

BatImporter is a universal, modular tool which allows e.g to merge the recording data, that is being imported with meta-data provided in a CSV file.


You can only import wave files (that were recorded without compression algorithms!). Files ending in capital letters (-.WAV) will have to be renamed to lowercase extensions (-.wav). BatImporter will do that for you.


Figure 15: Starting conversion of non-BatLogger data through the included BatImporter with the green Convert button (here at the lower right) from the Overview layout.


Figure 16: Dialog to chose Converter type (foreground window) and thereafter select your SD cards to be im ported (background window).

Once you have chosen your data folder (SD card), you may generate a sample CSV file (Comma Separated Values). This will contain the names of the wave files found, with empty columns for various meta-data to be filled in if desired. If no additional data are provided, some fields will remain empty in BatScope.

You will be asked to enter any recording speed adjustments that apply, e.g. when a slowed down playback was recorded to a wave recorder. The sampling rate of the data will be converted accordingly to the 312.5 kHz used in BatScope.


If you enter a wrong correction factor, your classification will go wrong badly. Cross-check BatScope‘s measured frequencies of a reference recording (e.g. Pipistrellus pipistrellus: peak frequency = approx. 45 kHz) after the conversion, to confirm correct speed adjustment, before treating amounts of data!

After successful import, your foreign data will show up in BatScope as sequences like the ones recorded with a BatLogger. Further processing works identical to BatLogger recordings.

The Layouts

In the top left of any window a popup-menu allows access to all the layouts, that will be treated in the following, step by step.

Figure 17: Available layouts in BatScope.


This is the first window that gives an overview over the hierarchy of your stored data.

Figure 18: The Overview layout.

From this layout you can:

  • Top row:
    • Create new projects,
    • Integrate projects folders already created by BatScope , e.g. when exchanging data, and
    • Sort Projects and SD cards.
  • Left side - Projects:
    • You can Edit project’s paths here, e.g. when they have been moved in the Finder to another folder or volume.
    • You may also Move projects directly from this layout,
    • or Delete projects.
  • Middle - SD cards:
  • Right - SD cards:
    • Within SD cards, you can Rename them,
    • Move them to another project, that already exists in the active database, or
    • Delete them.


Mind the interactive texts all over the layout! The cursor changes to a little hand over active elements and after a short while a little Pop-up Help will give some tool tips about the element’s functionality, e.g. jumping to the project’s folder in the Finder or showing all calls of that project. Explore!

If your data were recorded with a BatLogger, that contains an integrated GPS and writes meta-files to a route.kml file, you can view all recording locations in Google Earth by pressing the Earth button. The button does not work on foreign data.


Figure 19: Examples of recording locations’ viewed in Google Earth.

Sequence List


Figure 20: Sequence List layout.

This layout allows to quickly overview a series of recorded sequences.

At the top you may sort the sequences along several possible parameters, in ascending or descending order.

You can also select or deselect all sequences or invert the present selection.

The process menu allows you to perform different actions on the selected sequences, including export options.

The Filtering Records options allow you to narrow or widen the displayed sequences, by filtering on a variety of parameters:

  • Species (in different options). You may also choose a Genus here.
  • Project and SD card, the latter only being available after having chosen a project.
  • If Notes are empty or contain information.
  • the Status of sequences (enabled, disabled, marked to delete),
  • If sequences are Selected or not.
  • If they are already Cut or Classified or Verified.
  • Filter by the number of used Classifiers, the Frequency of the first recognized species,
  • the Quality of the first recognized species,
  • the average Signal to Noise Rate SNR of the sequence,
  • the Duration of the recording,
  • the time period the recordings were performed or imported by choosing the From date and the To date or the Import date respectively.
  • Finally the number of Calls tot. (total) in the sequence can be filtered as can the number of Calls ena. (enabled) and the N. species (number of species) found in the sequence.

All these filter options can be performed either as Normal search option, which searches over the whole database. Alternatively, you may use the filtering as an additive option to Extend the present selection or as subtractive option to Constrain the present selection. Finally by marking Omit, the set found by the filter will be excluded from the present selection. All except Normal work on the presently found set of sequences.

Here as in all other layouts too, many texts are links! Here, when clicking in the left pane the following actions are performed:

  • Project name jumps to the corresponding project in the Overview layout.
  • SD card name filters all sequences of that SD card.
  • Sequence name shows the corresponding sequence file in the Finder.

Clicking on the spectrogram will jump to the Single Sequence layout displaying the recording information.

On the right side of the spectrogram, above the buttons for Select/Deselect, Enable/Disable and mark to Delete (see also Call states), the recording date and time will be displayed, as well as its duration.

The small square to the right of this information indicates if the sequence has already been Cut and classified with either of the three classifiers SVN, KNN or QDA (see Classification Background).

The most right part displays the number of Total calls and presently activated Calls. Total Calls and the count will turn yellow, when calls are deactivated for the statistics in the sequence (see Call states). Clicking on either of these numbers will switch to the Call List layout showing the list of corresponding calls.

In this pane you also find the number of Species classified in this sequence and the name of the Most frequent species is indicated. Finally, some summary statistics are indicated, namely the Abs. (absolute) number of calls of the indicated species, the absolute Freq. (frequency) of this species’ call in the sequence and the average Qual. (recognition quality) of the species. (For further reference see also Classification Statistics).

Single Sequence


Figure 21: Single sequence with Detailed View of the spectrogram of a sequence.

This layout gives a detailed overview over a sequence’s data. The six visible panes explained:

On top are the the buttons for Select/Deselect, Enable/Disable and mark to Delete of the sequence (see also Sequence states), following buttons for Sorting the presently found sequences and a button to freshly Calculate and Save the sequence’s data.

In the middle left there is a pane for Navigation that allows to quickly jump to Overview or Sequence List layouts. The text to the right are again links! When clicking on the text in the pane the following actions are performed:

  • Project name jumps to the corresponding project in the Overview layout.
  • SD card name filters all sequences of that SD card and jumps to the Sequence List layout.
  • Sequence name shows the corresponding sequence file in the Finder.
  • Call numbers displays the corresponding calls in the Call List layout.

In the middle right pane the spectrogram and eventual final classifications are displayed. Clicking in the spectrogram will switch to Call List layout displaying all calls of the sequence. Besides the spectrogram the indication of Duration, Sample rate and Bits per sample can be found. Just below these values you will find buttons to Open the sequence in Raven, play it back slowed down (reduction factor to be set in Preferences layout; default = 10), and stopping the playback.

In the lower left pane there are two parts:

  • In the Calls section, you find on top the
    • classification statistics which give a summary over the number of calls (linked again!). Pressing the Details button will switch to the Classification Statistics.
    • Found species below indicates (maximum) three most frequently classified species and their statistics.
    • Below again you will find some information on the Cutter settings and versions of the call Inspection system and the Classification system as well as the Classifiers included. Finally that analysed this sequence and its calls, followed by an indication of the Signal-to-noise ratio of the calls in the sequence.
  • In the Verification pane are indicated
    • the three most frequently automatic classified species are indicated. Clicking on the green button will accept the species as Final classification. You can Manually override the automatic classification by choosing either long abbreviations popping up under the wider grey buttons, or by choosing the three-letter acronyms in the short abbreviations grey buttons - read also Note below!.
    • Final classification shows the names of maximum three verified species; If you find more species in the recording, you will have to resort to the Notes field. The Reverify button allows to reverify any verification, that might have become outdated due to deactivating calls. Finally to the right you will see if this sequences was classified and verified automatically or manually.


Open the small short abbreviations buttons list, either by Keyboard Shortcut or by clicking the button. Then quickly type the three-letter acronym of your species (complex or genus; see Names layout) and hit the Enter/Return key to accept that name. With another Keyboard Shortcut you switch to the next sequence. This is a very efficient way of verifying your sequences.

In the lower middle pane Recording date and Time are indicated as well as the Survey date. The latter is giving the date of the previous day for all recordings between 00:00h and 12:00h, to allow to select recordings of a full night. The survey date is thus the date of dusk of the night of recording. Import date are given in this pane as well as BatLogger specific values like Serial no., Firmware version, Temperature in degree Celsius and the Battery voltage oft the BatLogger at the time of recording.

Further BatLogger specific settings and trigger values are given below that information. Please refer to the BatLogger manual for more detailed information about the values. To the left you will find GPS data, if recorded by a BatLogger. Latitude and Longitude are given in World coordinates and Swiss coordinates (CH1903). Altitude above sea level and precision of the location measurement HDOP and number of Satellites considered are also provided.

In the lower right pane you find either in a Detailed View an enlarged display of the sequence spectrogram, or a Map of the recording location.


Figure 22: Single sequence with Map of the recording location of the sequence.

The Map presented corresponds to the recording location as presented by Google Maps (see copyright © at the bottom of the map). The Map window allows to zoom in and out of the location with the (+) and (-) buttons at the upper left. The text at the bottom below the map allow to Rest the Center and switch the map view between Normal, Terrain, Satellite, and Hybrid.


You can set the default view to Map or Detailed View in the Preferences layout !

Call List


Figure 23: Call List layout.

The Call List gives an overview of a selection of calls, e.g. those of one sequence. However, its most powerful use is the project wide filtering of calls of certain criteria to exclude them from the sequence statistics, thus improving classification quality. You can scroll through the list of calls and the top (Filter etc.) and bottom part (sequence spectrogram) will remain steady.

As in the Sequence List layout the top part offers to Sort the displayed calls by different fields, including measured parameters of the calls (Duration, Interval, Bandwidth, Max. frequency, Min. frequency and Peak frequency, SNR).

Calls can be selected/deselected (either All, None or the Invert of the present selection.

Processes that can be applied on the selected calls include:
  • Show sequences will switch to the Sequence List layout with the selection of all sequences, which calls are presently flagged as selected.
  • Export to Excel will export all measurements of the calls to an Excel spreadsheet. This export includes many more parameters than are visible in BatScope layouts!
  • Export calls will export just the selected calls to a location you indicate. At that location, the export will retain the hierarchy of the original data. This is to a) easily find the context of your exported calls and b) to allow exporting of potentially duplicate filenames.
  • Open in Raven Pro will open all selected calls at once in Raven Pro. See also External Helper Applications! This shortcut will only work with Raven Pro, no other External Helper Applications!
  • Enable will enable all selected calls,
  • Disable will disable all selected calls,
  • Mark to Delete will mark all selected calls for deletion.

The Filtering Records options allow you to narrow or widen the displayed calls, by filtering on a variety of parameters:

  • Species found by the classifiers. You may also choose a Genus here.
  • Project and SD card, the latter only being available after having chosen a project.
  • Sequence to focus only on a given sequence.
  • Classifiers, the number of classifiers used.
  • Agreeing filters the number of classifiers that agree on the species.
  • ø best delimits the classification quality of the best classifier.
  • ø species delimits the classification quality of the respective species.
  • Presence delimits the dominance of the found species.
  • CI tests filters on failed or pasted Confidence Interval test (see Judging and Improving Classification Quality)
  • Duration, Interval, Peak freq., and Bandwidth filter on the respective parameter.
  • Selected filters on the Select/Deselect state of the calls.
  • Status filters on the Enable/Disable and marked for Deletion state of the calls.
  • Seq. state filters on the Select/Deselect, Enable/Disable and marked for Deletion state of the corresponding sequence of the call.


Some of these filter options can be extremely powerful to eliminate weak classifications. These include Agreeing, Quality, SNR and CI test.

All these filter options can be performed either as Normal search option, which searches over the whole database. Alternatively, you may use the filtering as an additive option to Extend the present selection or as subtractive option to Constrain the present selection. Finally by marking Omit, the set found by the filter will be excluded from the present selection. All except Normal work on the presently found set of calls.

Here as in all other layouts too, many texts are links ! Here, when clicking in the left pane the following actions are performed:

  • Project name jumps to the corresponding project in the Overview layout.
  • SD card name shows all sequences of that SD card in the Sequence List layout.
  • Sequence name shows the corresponding sequence in the Single Sequence layout.
  • Call name shows the corresponding call file in the Finder.

Two spectrograms of the calls are presented, the raw spectrogram to the left and the filtered spectrogram to the right. Measurements are taken from the filtered spectrogram. Clicking on either spectrogram will jump to the Single Call layout displaying the call’s most detailed information.

On the right side of the call’s filtered spectrogram the buttons for Select/Deselect, Enable/Disable and Mark to Delete (see also Call states) are displaid.

Following that to the right in the Properties pane, the main call characteristics are indicated, namely Max. freq., Peak freq., Min. Freq., Duration, Bd.width, and SNR.

Following to the right again, in the Classification pane the abbreviation of the used classifiers are shown. In the present case these where all three SVM, KNN and QDA. Indicated in the same context are the Most likely species, the overall Confidence or quality of this classification and the number of Agreeing classifiers on the species.

Finally, in the right most Statistics pane a small review on the classification is given, Avg. best... classification rate over all classifiers, Avg. this species over the whole sequences, the number of calls assigned in this sequence to the same species as the call in focus, and if the 95% CI tests passed or failed.

At the bottom, a small preview of the sequence is given highlighting the position of the active call. This is again an interactive element: Clicking in the upper halve of this spectrogram will switch to the Single Sequence layout, clicking on the lower halve will switch to the Single Sequence Large layout !!


Some statistical call classification values are not shown anymore, when a call has been Disabled, as they do not make sense. At the same time, the summary textual information about the sequence at the bottom is shown in red.

Single Call


Figure 24: Single Call layout.

This layout gives a detailed overview over a single calls’s data. The six visible panes explained:

On top are the the buttons for Select/Deselect, Enable/Disable and mark to Delete of the call (see also Call states), following buttons for Sorting the presently found calls and a button to freshly Calculate and Save the call’s sequence’s data.

In the middle left there is a pane for Navigation that allows to quickly jump to Overview or Call List layouts. The text to the right are again links ! When clicking on the text in the pane the following actions are performed:

  • Project name jumps to the corresponding project in the Overview layout.
  • SD card name shows all sequences of that SD card in the Sequence List layout.
  • Sequence name shows the corresponding sequence in the Single Sequence layout.
  • Call name shows the corresponding call file in the Finder.

In the middle right pane the spectrogram of the sequence and the Position in Sequence of the active call are shown. Clicking in the spectrogram will switch to the Single Sequence layout of the sequence.

In the lower left pane there are three parts:
  • The Original spectrogram of the echolocation calls to the left.
  • The Filtered spectrogram of the call. All parameters are measured from this filtered spectrogram, except the intervals.
  • A graphic representation of the five Binned trajectory features of the call. Frequency parameters and steepness of the spectrogram slope are measured in this trajectory for the classification.
The lower right pane is again split into sub-panes:
  • Properties indicates the General properties of the call, mainly Duration, Interval to previous, Interval to next, Bandwidth, Maximum frequency, Peak frequency, Minimum frequency, and Signal-to-noise ratio. For reference, the used Analysis Tools are also given.
  • The Classification pane indicates the Total statistics as given in the Call List layout. These are the Most likely species, the overall Confidence or quality of this classification and the number of Agreeing classifiers on the species. Just below that, detailed results are given for each of the used classifiers Support Vector Machine, K nearest Neighbors and Quadratic Discriminant Analysis. These are the Best and Second best fitting species name, its corresponding classification quality, and the result of the 95% CI tests.

Single Sequence Large


Figure 25: Single Sequence Large layout..

This layout fuses features of the Single Sequence layout and the Call List layout into one. It offers quick overview over the sequence’s data, the contained calls and allows to do verifications. Furthermore it gives a bigger view of the full sequence and indicates the position of the presently selected call within the sequence. This overlay can be switched off with the Show overlay option.

Access to the Notes field is possible here too.

Detailed description of the Navigation pane can be found under Single Sequence layout.

Detailed description of the functionality of the call listing in the Calls pane can be found under Call List layout.


Mind all the Keyboard Shortcuts that will speed up your work in this layout, which may be the most efficient one for verifying large amount of data.



Figure 26: Names layout.

This layout simply displays all known species, species complexes and genus names known to this version of BatScope. Short Names and Shortcut Names are used in the manual verification or classification procedure (see also Single Sequence).



Figure 27: Macros layout.

This layout is meant as a means to streamline repetitive tasks e.g. filtering out noisy calls, such that failed CI tests, or which are in undesired parameter ranges.

The layout is included for WSL to be able to design macro steps that will be made available to the public in the future, once they are tested thoroughly.

By default the layout is deactivated, but access can be granted through the Preferences layout. At present, we do not offer any support whatsoever for this layout.



Figure 28: Preferences layout.

In this Preferences layout you can set a few parameters and trigger final deletion of sequences and calls.

  • Cutter Settings allows to adjust the sensitivity of the cutter to noise. Do only set these values if you are knowing what you are doing. We highly recommend to stick with the default values.

  • External Software Settings allows you to indicate either the Path to either Raven Pro (if moved out of the /Applications/ directory) or an alternative External sound application to view and further analyse your recordings. If your Raven installation is within the default location (/Applications/ directory), BatScope will find it automatically - no need to enter the fields.

  • Under Delete Files you can choose
    • if files to be deleted should be first Moved to the Trash - this happens quicker and you can later empty the trash asynchronously,
    • or Deleted directly by the UNIX ‘rm’ command. This may take a considerable while, if you have many hundred sequences with cut calls to be deleted.

The red buttons will start to Delete Sequences Marked for Deletion (including associated calls!) or to Delete Calls Marked for Deletion.

  • Other summarizes various settings:
    • Audio playback deceleration sets the slow-down factor for the playback of sequences and calls.
    • File delimiter... allows to set the delimiting character in CSV files from BatScope.
    • Title... allows to set the program string to be displayed in the windows header, either just the filename of BatScope (remember, you may rename it for further structuring of your date), or the full pathname, which may better serve mnemonically and make it easier to retrieve the program started.
    • Default tab... gives you the choice of Map or Detailed View as default pane in the Single Sequence layout.
    • Enable learning layout will allow to access the Learning layout.
    • Enable Macro layout will allow to access the Macros layout.


Neither Learning nor Macros layout are presently supported !



Figure 29: Learning layout.

This layout is designed for experts only, who want to compile an own library of reference calls for learning and later classifying.

The access to this functionality is included for WSL to be able to improve the classification in the future.

By default the layout is deactivated, but access can be granted through the Preferences layout. At present, we do not offer any support whatsoever for this layout.

Keyboard Shortcuts

External Helper Applications

Google Earth and Google Maps

If your data were recorded with a BatLogger, you will be able to view the position of all recordings of a given SD card in Google Earth from the Overview layout.

BatScope makes use of the API interface of Google Maps to view recording locations inline in the Single Sequence layout map pane.

Sound Analysis

BatScope provides an interface to alternative sound analysis software. You can indicate the path to the package of your choice in the Preferences layout. From own experience we recommend Raven Pro, but others will also work. We illustrate here two possible solutions:

Raven Pro

Raven light is a simple solution to view and explore sound files in the time and frequency domain in different resolutions than BatScope offers.

In contrast, Raven Pro offers full fletched and customizable analytical options up to automatic signal detection and measurement.


Figure 40: Raven Pro window of a bat echolocation sequence. The software offers extensive tools for display, analysis and playback etc. of sound files.


Figure 41: Raven Pro window of a series of bat echolocation calls passed directly from within BatScope by the Open in Raven Pro process in the Call List layout. Individual calls are separated by light green dashed lines.

Both programs were created in the academic research environment of Cornell Universities Lab of Ornithology, were Raven can be obtained.


The manual included in Raven contains two very informative and noteworthy sections appended (A + B) on Digital Representation of Sound and A Biologist’s Introduction to Spectrum Analysis that are highly recommended reading!


Amadeus is a wave editor that offers also spectrogram viewing. It allows some customizing like zooming into time and frequency domain, but Amadeus has no interface for measuring parameters.

Figure 42: Time and spectrogram window of a recorded bat echolocation sequence, as they can appear in Amadeus.

Known Problems


As mentioned under Judging and Improving Classification Quality: BatScope does not tell you the unquestionable truth! Be aware of the variability included in echolocation of bats. Do judge the results of BatScope classifications critically and control the results before verifying them. You can always opt on the save side and manually classify to a more certain level like species complex, genus or even genus complex.


  • Problem: Buttons in BatScope become unresponsive, if the active record has moved far away from the focus, e.g. by scrolling in a list in Sequence List or Call List layouts. This is a known bug in the FileMaker© engine enclosed.

    • Solution: Click anywhere into the dark grey area of a visible record (not onto a button or text) to activate that record within the visible range. The buttons should immediately work again.
  • Problem: Button Earth in Overview layout will throw an error if the recordings where not done with a BatLogger, as the route.kml is missing.

    • Solution: None at the moment. Either a more graceful message or a new functionality might cure that in an upcoming version.
  • Problem: Exporting classification data, that contain special characters (ä, ö, é, ç, etc.) will export these characters scrambled in the spreadsheet file - for Excel versions below 2011 and Numbers.

    • Solution: None at the moment, apart from the unsatisfactory recommendation to NOT use special characters at present. The problem seems tricky and dependent on software used to read the data later (Excel, Text Editor, Numbers,...). An upcoming version will fix that issue.
  • Problem: After having imported data from a NON- BatLogger device, in general you will not have geo-referenced meta-data. Correspondingly, the default tab in the Single Sequence Layout will show an empty Map pane.

    • Solution: Got to Preferences layout and switch your default tab in the Single Sequence layout from Map to Detailed View (third last entry in Other pane of the layout - as of V.3.0.16, rev. 11.01.2013). Thus you at least get some additional information in the respective tab of the layout.


  • Problem: Data imported into BatScope from non-BatLogger devices will nevertheless show eventually entered meta-information in the Single Sequence layout under the description BatLogger.

    • Solution: None at the moment, partly because we have no guarantee to know, what device foreign data came from. We try to work out a solution for dynamic renaming of the corresponding label in a future version of BatScope.
  • Problem: In the Sequence List layout the classifier Support Vector Machine is abbreviated as SVN instead of SVM.

    • Solution: This is a typo, just ignore it and interpret as SVM. Due to possible consequences of changing this string, we have to further test the correction and will only fix the corresponding label in a future version of BatScope.

Final Words


BatScope came to life to offer our experience and knowledge of bat bioacoustics to a wider community of biologists, who are working increasingly with automated devices like the BatLogger. The development of the latter (in cooperation with ELEKON AG) and parts of BatScope was financially supported by an Environmental Technologies Development grant of the Swiss Federal Office for the Environment (FOEN).

We gratefully acknowledge the testing of and critically commenting on many versions of BatScope by Annie Frey-Ehrenbold and Fabio Bontadina (SWILD), Hans-Peter B. Stutz and Hubert Krättli (Fledermausschutz CH), Thomas Sattler, Raul Rodriguez, Peter Zingg, Emmanuel Rey, Elias Bader, Martin Decurtins, Carsten Braun, and the many other registered users of BatScope.


The Swiss Federal Institute for Forest, Snow and Landscape Research WSL offers the BatScope product as is with no warranties and no liabilities.

BatScope 3 Documentation Revision History

Revision 1.0 - 2012-12-18

Revision 1.1 - 2012-12-24

Revision 1.2 - 2013-01-08

Revision 1.3 - 2013-01-08

Revision 1.4 - 2013-01-23

Revision 1.5 - 2013-03-01

Table Of Contents

Previous topic

Welcome to BatScope’s user documentation!

This Page