This function exports all the information of the BioVis3D sequence to tab-separated values text files, which then can be imported by applications such as Microsoft Excel and OpenOffice Calc, as well as a text editor or a scientific software.
Three text files are saved, each with different types of information:
Sequence Export.txt - This file includes information about the sequence properties, as well as detailed information about its elements, including measurements.
Sequence Export - Contours' Traces.txt - This file includes the space coordinates of the traces for each contour of the sequence.
Sequence Export - Paths.txt - This file includes detailed information about the paths of the sequence, including their measurements.
To export the information of the opened sequence:
1 - Select the option Export Sequence from the File Main Menu.
2 - Check/uncheck Recalculate outdated contour measurements, Recalculate outdated object measurements and Recalculate outdated path measurements check boxes. By default, BioVis3D recalculates the measurements affected by user changes. If the outdated measurements are not relevant at the time of generating the exportation, the process can be speed up by unchecking the corresponding options. When recalculation is not requested, the outdated values are shown as n/a (not available).
3 - Press the OK button and select the directory and the file name for the exportation.
The coordinate system used by BioVis3D is the Cartesian coordinate system, where axes are oriented as shown in the Figure 1.
1: The coordinate system used by BioVis3D.
Please note the following when importing text files to a spreadsheet or scientific application:
The information is saved starting in line 1.
The information is delimited with tabs within each line of the text file.
The decimal separator used is the period (.), regardless of the decimal separator configured in the computer. The decimal separator needs to be configured when importing the information for proper number interpretation. Then, the thousands separator needs to be configured to be the comma (,), although BioVis3D does not use it.
The file Sequence Export.txt
The first section of the file includes summary information of each object and each dot set in the sequence. This includes quantitative information such as volume and surface area for each object, as well as the number of dots for each object, and the number of dots for each slice. The second section includes detailed information of the sequence. This includes the objectís area and perimeter in each slice, and the position of each dot for each dot set.
Important note: If an object contains dot sets, the volume and surface calculation does not include the dot sets.
Figure 2 shows the exportation of a sequence for three objects, Brain, Magnocellular and Spherical cells, being that the object Spherical cells is the only object that contains dot sets. Please note that formatting was included and several lines were removed for better visualization.
Figure 2: Exported information with formatting.
The file Sequence Export - Contours' Traces.txt
This file contains the traces of the contours for each object of the sequence. The traces are the contours as drawn in the Slice View at a zoom factor of 100%. This means that consecutive coordinates are adjacent in the display coordinate system (pixels).
Each line in the file contains a point of the trace. The point is given by its coordinates in the X, Y and Z axes, expressed in the unit of measure of the sequence and in pixels.
Figure 3 shows the exportation of the contours' traces for the object Brain, for the slices 1 and 2. Notice that formatting was included and several lines were removed for better visualization.
Figure 3: Exported information with formatting for contours' traces.
The file Sequence Export - Paths.txt
This file contains the sequence's paths information. See Measuring a path for detailed documentation.