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Data Structure

Introduction

The function of the data structure is to store all the information and data about the experiment in an easy to recall place. Note that the structure has one cell per row and that if dual color data is loaded the two channels will be stored in the same row. It is divided in two components: a Data structure and an Info structure, where the former collects all the data and the processing results, and the latter stores all the information concerning the experimental design and imaging paradigm.

Overview of the Data structure

The data structure collects the raw data, as well as derivative measurements of those data. It has a structure that allows the storage of multiple cells and conditions, as well as multiple protocols. The core fields will be present when data is loaded, and additional fields will be added when detection, localization and classification will be performed. The data structure after importing will contain the following fields (the following structure is for container version 1.5, see the about dialog):

Overview of the data structure
Figure 1: Overview of the fields in the data structure. Required fields are displayed in green and red, for the primary and secondary color, respectively. Optional fields are indicated by a yellow or orange color, depending on the presence of synaptic information or the presence of ROIs.

The following is a brief description of the fields, which are created after importing the data has completed:

After processing the data using the fusion detection, six additional fields will be added to indicate the results from the processing. The fieldnames in this list indicate the names for the fields of the primary color, and some will have a counterpart when dual color is present, as indicated by the [1,2] for the following list:

Dual color

When a data set with two colors was loaded, the import function will generate separate fields for the primary (pHluorin) and secondary (mCherry) color, as indicated in Figure 1. When performing the fusion detection, the fields for events will also have separate fields for onset of the events and the goodness as indicated above. Some of the settings for detection of events are separate for the primary and secondary color, as described in the documentation of the detection module. To create a data set for dual color, refer to the template creator documentation for more information.

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Info structure

General information

The InfoStruct has three sub-structures that contain all the information concerning the experimental procedure and acquisition (protocol), the associated physical units of the experiment (units), and finally the meta-information about the experiment (general). The fields for the sub- structures are shown in Figure 2, and are based on the information provided by the Infosheet in the selected Excel file.

info structure
Figure 2: Fields of the InfoStruct.
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Protocol

The Protocol structure stores the information concerning the acquisition and stimulation protocol. Calculation of times in the interface and plots (duration, onset) use the AcquisitionTime field to convert frames to physical units (seconds). An incorrect value will result in unexpected results. If data needs to be combined that contains different time intervals, it needs to be imported via separate files, each with their own Infosheet containing the correct values for all cells contained within it. Every unique protocol will get its own index value that is stored in the expInfo field of the corresponding cells in the main data structure (Figure 1). This will also allow for cells acquired using different stimulation protocols to be combined in one data set.

The stimulations considered thus far are: field stimulation (named field), high potassium (k), calcimycin (cal) and sucrose; ammonium (nh4) is always considered to be present. The data placed in 1 Excel file are assumed to have been acquired with the same protocol and intervals.

Units

The units structure stores the physical units that were used for the acquisition. Time interval can be supplied in seconds or Hz (1/s), and will be used to switch from frames to physical units, and vice versa. Setting the units correctly is important for a correct analysis of the data; the program uses frames as the only unit internally. To measure onset time and duration, it will convert the frames to physical units before presenting the data. However, as stated in the loading information as soon as the units are provided in the Excel file, the program will take care of them and adjust the value if necessary.

General

The information stored in the General sub-structure is more for a general overview of the microscope used and the cell background; useful for a general comparison between users. The values in this sub-structure do not influence the results of the data processing. Of particular importance is the "synaptic" field; this will tell the program that inside the Excel sheets it will find also the intensity of the synaptic marker for each ROI of each cell, as explained in the template creator.

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Silent structure

The interface allows the user to add non-releasing cells (silent cells) to the data set. Silent cells can be added per condition and also per cover slip. The latter option is only important for more advanced statistics using a multi-level approach (see the statistics documentation for more details). The interface consists of a field where the number of silent cells can be entered and a selector for the condition and the sheet ID:

silent interface
Figure 3: Interface for adding silent cells.

After pushing the button, the cells will be added and a dialog will show how many cells were added to which group as a confirmation. When closing the interface, the results will be pushed to the main interface and will be stored in the session file if auto-save is enabled. It is also possible to remove silent cells that were added by selecting them and pressing the Delete cell(s) button.


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