A description of the file formats of the different available reports.
Most report types can be requested for a whole project as well as for individual volumes. A project report is a convenience feature which requests reports for all individual volumes of the project at once and provides a ZIP file containing the volume reports for download. However, not all configuration options may be available for project reports.
The following sections describe the different types of volume reports but, per definition, apply for project reports as well.
The basic annotation report contains a graphical plot of abundances of the different annotation labels (annotations can have multiple labels by different users). If the annotations should be separated by label tree, there will be one plot for each label tree that was used.
The bars of the plot are color-coded based on the colors of the labels they represent. If any label occurs more than a hundred times, a logarithmic scale is applied.
The extended annotation report is an XLSX spreadsheet which contains a list of the abundances of each label and image. If the annotations should be separated by label tree, there will be one worksheet for each label tree that was used.
For a single worksheet (not separated by label tree) the first line contains the volume name. For multiple worksheets the first lines contain the name of the respective label tree. The second line always contains the column headers. The columns are as follows:
The label hierarchy contains all label names from the root label to the child label, separated by a >
. If we have the following label tree:
Animalia └─ Annelida └─ Polychaeta └─ Buskiella spThen the content of the "label hierarchy" column for annotations with the label "Buskiella sp" will be
Animalia > Annelida > Polychaeta > Buskiella sp
.
The annotation area report is an XLSX spreadsheet of all area annotations (rectangle, circle, ellipse and polygon) with their width and height in pixels (px) and their area in px². If a laser point detection was performed, the width and height in m and the area in m² is included as well.
For a single worksheet (not separated by label tree) the first line contains the volume name. For multiple worksheets the first lines contain the name of the respective label tree. The second line always contains the column headers. The columns are as follows:
The full annotation report is an XLSX spreadsheet similar to the extended report. It contains a list of all annotations and their labels.
The columns are as follows:
For the different annotation shapes, the coordinates are interpreted as follows:
The CSV report is intended for subsequent processing. If you want the data in a machine readable format, choose this report. The report is a ZIP archive, containing a CSV file. The CSV file name consists of the volume ID and the volume name (cleaned up so it can be a file name) separated by an underscore. If the annotations should be separated by label tree, there will be one CSV file for each label tree and the CSV file name will consist of the label tree ID and name instead.
Each CSV file contains one row for each annotation label. Since an annotation can have multiple labels, there may be multiple rows for a single annotation. The first row always contains the column headers. The columns are as follows:
The annotation points are encoded as a JSON array of alternating x and y values (e.g. [x1,y1,x2,y2,...]
). For circles, the third value of the points array is the radius of the circle.
The additional attributes of the image are encoded as a JSON object. The content may vary depending on the BIIGLE modules that are installed and the operations performed on the image (e.g. a laser point detection to calculate the area of an image).
The basic image label report is an XLSX spreadsheet similar to the extended annotation report. It contains a list of all labels attached to each image of the volume. The columns are as follows:
The CSV report is similar to the annotation CSV report. If you want the data in a machine readable format, choose this report.
Each CSV file contains one row for each image label. Since an image can have multiple different labels, there may be multiple rows for a single image. The columns are as follows: