This module orchestrates hardware interactions with Patch Clamp Amplifiers and Camera Modules to acquire patch-clamp data and fotos/videos. BPE can communicate with Patch Clamp Amplifiers to trigger recordings and import the generated data into the BPE database immediately. So far, communication with Amplifiers from the HEKA company is supported and requires a valid version of Patchmaster v2x90 as well as preconfigured pulse generator- (.pgf), protocol- (.pro) and analysis files (.onl). We are currently working on the integration of PatchMaster Next too.

Batch Communication between BPE and HEKA EPC Amplifier

1. Principle of Communication

As illustrated below in Fig. 1., the communication between Patchmaster (PM) and Biophysical Essentials (BPE) works via specific *.in and *.out files. Therefore, PM and BPE must share access to the directory of these files. In case of selecting the shared path on a network resource, PM and BPE can even operate from different computers.

2. Set up PatchMaster (PM)

Open Patchmaster, go to the configuration tab and select the path for the .in and .out files. This path MUST be also accessible for BPE.

Once the path ist set correctly, the batch communication can be enabled by checking the respective checkbox. In the notebook of PM, one can see PM searching actively for input files.

Set up Batch Communication in Biophysical Essentials

BPE can write specific control sequences into the .in file which will be interpreted by PM and the specific command will be executed.

Therefore, the respective .pgf, pro, and .onl files muste be selected as well as the path where the .in and .out file will be generated/modified.

Once all paths are set, a connection with the amplifier can be initiated and if successfull, the window will change to the different control sequences. By drag and drop, pre-configured series or protocols can be selected and exectuted.

The online analysis (ONA) module serves as a basic file viewer for single patch-clamp recordings. Once opened in the ONA viewer, the recording files can be directly imported into BPEs permanent database using the transfer interface. Additionally, a labbook interface is provided. The labbook visualizes actual recording parameters and provides the option the add additional comments.

This module supports the import of existing recording data, filtering, analysis, visualization and statistical analysis.

1. Start a new Offline Analysis

To start a new offline analysis, select your recordings of interest from the Data Dashboard. Data can be grouped and selected by the given meta data which can be changed in the dropdown menu. Individual recordings and other grouping cirteria can be selected by SQL queries in the second tab of the data dashboard. For each started offline analysis, an unique offline analysis id will be assigned by which all actions will be re-trackable.

2. Data Control

The data import process is complete when a treeview listing all experiments and a data view with related visualizations appear on the screen (see Fig. X). To maintain maximum control over data and downstream analysis, BPE offers numerous options for manual visualization, filtering, and selection. These options help ensure high-quality analysis and trustworthy results.

2.4 Rename Series Name

You can rename a Series by clicking on the "rename-series-button". This will bring up a dialog that allows you to select a series to rename from a dropdown menu.The dropdown is generated automatically from all available series names at the time you open the dialog. To input a new series name, simply type it in and select whether this change should be temporary for this analysis only, or a permanent change to be written into the database.

3. Data Analysis

To start an analysis, at least one series must be selected. For each selected series, a specific analysis window is generated and allows to stack the analysis of all seriers of interest. The analysis configurator allows provides a new tree- and a data view which is this time specific for the seleted series. BPE automatically detects whether the available analysis functions for the selected series by differenciating between voltage and current clamp. A full list of available analysis functions is provided in Tab. .. , and can be generally sepated into general and series specific analysis functions. Voltage clamp recordings are usually normalized to the CSlow paraemter of the cell membrane capacitance componsation while current clamo For each analysis function, an analysis interval can be selected by draggable cursor bounds which will be applied to all selected data. This allows highly conserved data analysis comapred to the classical workflow.

Each analysis result represents a single value (y-ccordinate) while the x-Axis is dependented on the provided data. In case of a step protocol, one might to plot the results according the related or voltage stage, or e.g. against the current ramp in a ramp protocol. Therefore, the user can select an interval that was read from the pgf file.

To increase the transparancy of the anaylsis functions, an implemented live plot mode allows to apply analysis functions immediately to see the output of the selected analysis.

Analysis Functions

4. Statistics Module:

The following statistical tests can be performed

1. t-test_ind (Independent t-test):
   • Use when you have two independent groups.
   • Assumes that the data in each group is normally distributed and has equal variances.
   • Use this test if the assumptions are met; otherwise, consider using the Welch's t-test or non-parametric tests.

2. t-test_welch (Welch's t-test):
   • Use when you have two independent groups.
   • Similar to the t-test_ind but does not assume equal variances.
   • It is more robust when the variances are unequal or the normality assumption is violated.

3. t-test_paired (Paired t-test):
   • Use when you have paired or matched observations (e.g., before and after measurements).
   • Assumes that the differences between pairs are normally distributed.

4. Mann-Whitney U test (Wilcoxon rank-sum test):
   • Use when you have two independent groups.
   • Does not assume normality or equal variances.
   • It tests if the distributions of the two groups are significantly different.

5. Mann-Whitney-gt (Mann-Whitney test for one-sided alternative):
   • Use when you have two independent groups.
   • Similar to the Mann-Whitney U test but tests for a one-sided alternative hypothesis.

6. Mann-Whitney-ls (Mann-Whitney test for a less than alternative):
   • Use when you have two independent groups.
   • Similar to the Mann-Whitney U test but tests for a less than alternative hypothesis.

7. Levene's test:
   • Use when you have two or more independent groups.
   • Tests the equality of variances across the groups.
   • If the variances are significantly different, it indicates that assumptions for parametric tests may be violated.

8. Wilcoxon signed-rank test:
   • Use when you have paired or matched observations.
   • It does not assume normality and tests if the differences between pairs are symmetrically distributed around zero.

9. Kruskal-Wallis test:
   • Use when you have three or more independent groups.
   • Non-parametric alternative to one-way ANOVA.
   • Tests if the distributions of the groups are significantly different.

10. Brunner-Munzel test:
    • Use when you have two or more independent groups.
    • It does not assume normality or equal variances.
    • Tests if the distributions of the groups are significantly different.

    Once all the settings are finished, clicking the run button will start the calculation and visualization of the reuslts. Therefore, the new items “P

The database viewer module allows you full access to the data - including recording file structure as well as numerical raw data and offline analysis results. All actions performed by a user are stored in this database and can be reopened at any time from the GUI to facilitate reproducible and transparent data analysis. For advanced data control, sql queries can be entered within the database viewer module as shown in the figure below. All data tables can be inspected from the GUI without the need of SQL-syntax.

Data can be imported into BPE from recording files as well as from other BPE databases (e.g. from another computer from yourself or a cooporation partner)

1. Data Structure

BPE considers a structure of:

2. Import multiple files from directory

In the current BPE release, HEKA files with '.dat' file extension and AXON's '.abf' files can be imported. The recording files will be interpreted from BPE and copied into the BPE-specific database, which runs in the background of the software. This database will be only available on your local computer. If you want to backup or upload your data, please read the section on Online Services and Data Export.

1. General Import Instruction

To import new data into BPE, click the offline analysis button in the main menu, click "load from directory"choose the respective data type and select the directory containing the recordings. Once selected, a dialog will appear asking you to either upload metadata from a (.csv) file or assign it within the dialog. We highly recommend setting metadata, at least for the experiment label, to distinguish data from each other. After clicking "continue," the displayed data will be added as metadata to the database. Importing data into the database requires some processing time, so be patient as this is the slowest process of the entire software.

2. Reading HEKA files

HEKA's .dat file format was changed in the past from an unbundled to a bundled version. BPE supports both formats. Very important: For unbundled format reading, the .pul and .pgf files need to be provided in the same directorey as the .dat file. Also, the naming must be identical except of the extension. Please be advised that HEKA provides a conversion from unbundle into bundled format within PatchMaster. Preferentially, each recording file contains a single experiment. BPE can handle HEKA files with multiple experiments, but the reading speed is decreased and will lead to an automated naming of the experiment too.

3. Reading AXON files

AXON's .abf files need to be renamed so that all file names of protocols that belong to the same cell start with the same string, followed by an underscore. For example, "cell1_....abf".

4. Reading NANION files

This feature is currently under construction and will be available in the next release around October 2024

2. Import data from existing database

BPE supports to exchange raw data and analysis results between different BPE instances. Therefore, data can be exported as described in the chapter Data Export. Data that were exported as described there, can be imported by starting an offline analysis, and clicking "open exsiting analysis". This will open a dialog which shows the option to import existing bpe_data.

Data can be exported from BPE in different ways. Single signal traces can be exported as .csv files, trace images and result plots can be exported as image or vector graphics. An entire analysis inlcuding raw data, analysis function parametrization and analysis results can be exported as database object.

Export a database object

Go to the database viewer module and select "Export Analysis" in the ribbon bar. A popup dialog will open to allow you to set the path directory where you want to store the db object and which analysis (identified by its ID) you want to export. Click "Export Datbaase" which will automatically export all the data that are linked with this analysis.

BPE is a young project with high potential to become included in many different Patch-Clamp projects in the future. However, it might happen that some features will not work for a specific use case, such as an unexpected input data format, different file versions or missing meta data in some amplifier systems. We strongly encourage you to report such use cases either as issue on the projects github site or by individually reaching out per email describing the details of the problem. Please don't hesitate to reach out, we are more than happy to support you and your data analysis. BPE is writing a status-and error-log file that might be helpful to be provided too.

Finding the log-file

Within your BPE folder, navigate as shown in the figure below to _internal/Logging/Logs and you will find the main log file titled "log".