The photo gallery below illustrates the range of analyses available in photoQuad, including random points, species markers, grid cell counts, and freehand or image segmentation-based species regions, coupled with some measurement tools, the quadrat boundary and the image's calibration marks.

If you were to put all of this together, the result would be a cluttered and difficult to comprehend image, pretty much like the (exaggerated) example below. Each of the aforementioned objects however operates on a distinct layer, which can be toggled visible when needed, and manipulated separately both from the underlying image and from the other analysis objects.

In summary, photoQuad's operation is based on two general editing levels: edits that regard the pixel values of the image, and edits that involve objects superimposed on the image. The first category includes the actions covered in the image enhancement section, namely contrast modification, image rotation, color balance adjustment, etc.

The second category encompasses practically every tool that the user superimposes on the image in order to extract or assess the biological/ecological information contained therein; the list includes:

• image segmentation species regions

• freehand species regions

• species count markers

• grid cell counts

• random points

• general-purpose measurement tools

• regions of interest (ROIs)

• quadrat boundary and image calibration marks

Each of the above categories can be analyzed, edited or deleted independently of the others, without affecting the underlying source image.

Layers can be saved/loaded using either the menu on the main image window, or the corresponding buttons on photoQuad's floating graphical user interface (GUI).

save/load layers using the File menu

save/load layers using the floating GUI buttons

layer filename is shown on statusbar

Important note:

All layer objects are saved as a single file in photoQuad's native format (*.Layer.pqd), and there is currently no option to save a particular layer slot. For example, if you have an image with the quadrat boundary, some species regions and random points, you cannot separately save the random points only. You save the whole layer structure into a single file, blank slots included.

Load layers

When loading a layer file, photoQuad performs an initial scan and identifies which layer types are present in the file, as illustrated in the example below. You can select which objects will be loaded using the respective checkboxes. Note that if you finally import an object of type X, it will replace all objects of type X in the current image, if any; objects of type Y, Z, etc will be left intact.

Important note:

When you want to use a layer file that corresponds to image A into image B, it is recommended that you do so at the beggining of the image B analysis, i.e. before you start drawing new objects on image B. Here's a typical scenario:

You define and calibrate the quadrat in image A, and you want to use that quadrat in all subsequent images (image B, image C, ..., etc). To do that, work in image A as normal and save the layers; the produced file will normally contain additional analysis objects from image A, e.g. random points and species regions. That's OK, leave them be. Navigate to image B, and before doing anything else load the layers from image A. Keep only the quadrat and disregard all other objects (the random points and species regions in this case), and then start working on image B. Repeat for image C, image D, ..., etc.

WARNING

When loading a layer file from disk, the software does not check if the species names and species IDs in the layer file match with the species library that is currently used.

It is the user's responsibility that the same species library is used both while saving, and while loading a layer file. If this doesn't happen, the layer file can still be loaded but the exported results may be inaccurate.