New User Tour

We will take a quick tour around PMbrowser, exploring typical use cases.

dektop icon

After successful installation (see Installing PMbrowser), you can start PMbrowser via the start menue or a link on the desktop.

You can open a PatchMaster (Next) dat-file via File –> Open... or by simply dragging the file onto the application windows. For this tour we will use the DemoData.dat file provided with the PatchMaster installation.

The Application Window (overview)

tour step 1

The application window is divided into three sections, the tree view, the graph area, and the text area (see screenshot [1]).

  • The tree view represents the tree structure stored in the dat-file. Groups (or experiments, the file format treats both the same), series and sweeps are represented as nodes, traces from the final leaves of the tree. Elements for which a label is stored in the file are named accordingly. Elements without a valid lable are automatically named, e.g. trace_1, trace_2

    The nodes can be collapsed by a single mouseclick on the v-shaped symbol or hidden via the context menue: right-click on the node to be hidden and select menu item hide subtree. A double click on any item will “play” all traces that a children of this item in the graph area.

  • Inside the Graph Area trace data will be displayed as soon as a trace has been selected in the tree view. Until then, it displays the text no data to display.

  • In the text area mainly metadata will be printed according to the element being selected in the tree view.

    The menuitem File –> Select Parameters... calls up the ‘Select Parameters’ Dialog which lets you choose for each level (group, series, sweep and trace) which metadata items PMbrowser shall print.

dialog select parameters

Browsing Trace Data

Now let’s explore some of the data. Click on some traces and / or double-click on a series item to populate the graph area. (compare screenshot below).

tour step 2

You will realize that the graph auto-scales according to the last selected / added trace. A certain number of “background” traces remains in an internal buffer of the graph display. You can influence the storage and display of these background traces and the autoscaling behavior (see below).

Selecting / Filtering Traces of Interest

Usually, we are not interested in all traces, e.g. leak traces might be less interesting. Let’s assume we want to specifically analyze traces from the “Tails” experiment stored in DemoData.dat that were done with the “Toff” protocol ( = “Toff” series). We are only interested in the currents recorded, i.e. “Imon” traces.

We go to the menuitem Tree –> Filter... to open the filter dialog. Change the Group, Series and Trace fields according to our whishes (see screenshot). Click “OK”.

tour step 3

Now all unwanted tree items and traces are hidden. Double-click on the tree item labled “3 Tails” to get a quick overview of the recording. (Menu Tree –> Show All will bring back the hidden items / traces.)

tour step 4

Exporting Traces to Igor

Now we want to export the traces that we selected in the previous step for further analysis in IgorPro.

Select menu item File –> Export All Visible Traces for Igor.... (All traces not hidden are considered visible.) In the Choose Path & Prefix dialog, we change the prefix to Tails. The names of the exported waves will now start with “Tails_”.

tour step 5 export dialog

Select the radio button “Export for Igor Pro” (not shown in image).

We want to create a single experiment file that contains all data. Also we want to create have datafolders according to the tree structure in this file. Therefore we select “create pxp file” and “create folder structure”. As last folder level we select “series”. This means that all sweeps and traces belonging to one series will be placed in one datafolder. (Since we have only one group and one series to be exported, we could do without the datafolders. But for this demonstration, we select this anyway.)

We do not change the “path”, as this only important if we want to export a bunch of ibw files.

Clicking “OK” takes us to a file dialog to select location and filename for the new pxp file.

Open the pxp file in IgorPro. (Versions older then 5 will not work.) In the Data Browwser you will see the datafolders and one wave for each trace.

In Igor’s Macros menu you will find the item Display Waves. Select this to automatically create graphs for all series that you imported.

Metadata will be included in the wavenotes of the imported waves. File –> Select Parameters... in PMbrowser will bring forth a dialog that let’s you choose which metadata-items to export in the wavenotes.