Frequently Asked Questions
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What is photoQuad?
photoQuad is a custom software for advanced image processing of photographic quadrat samples, dedicated to ecological applications. The system integrates all major 2D base analyses used in marine biology and ecology for studying biodiversity of sessile communities through photographic sampling.
Which analyses are included?
Pretty much every analysis that is commonly used for quadrat or photographic sample processing, including random point counts, species counts, freehand species regions, image segmentation-based regions, and grid cell counts.
What can I measure with all these analysis options?
You can extract quantitative information regarding the distribution and characteristics of organisms and associated substrate from image samples, including absolute area, percentage coverage, perimeter, advanced morphological descriptors, frequency of occurence, and species composition.
Can I use photoQuad for advanced statistical processing?
No. The software is designed to quantify the raw ecological information contained in image samples, and export the results to worksheets. What happens next with these worksheets is up to the user.
Is photoQuad free?
Yes.
Who built it?
Who maintains it?
How can I help?
If you find that photoQuad is useful to your research, there are many ways to contribute...
On what operating systems does photoQuad run?
The current version only runs under Windows, but we'll soon make it cross-platform (Mac/Unix/Win).
Which are the recommended specifications for a computer running photoQuad?
We've built photoQuad on an average machine for today's standards: MS Windows XP SP3, Intel Core2 CPU 6400@2.13GHz, 2.0GB RAM, 1024MB GPU. Software performance was excellent even with demanding operations such as image segmentation, hence that's our average recommended specifications. You can go for lower specifications, but having enough computer memory (≥1GB) is the most important factor here.
Which programming language was used to develop photoQuad?
MATLAB; but you don't need it, photoQuad is available as a stand-alone executable.
OK, I've got photoQuad running. How do I import an image and start working on it?
You now have this interface on your screen. Start by selecting a drive letter (i.e. directory mounting point) from the "Select drive" drop down menu. Use the directory tree to navigate to your source images, click an image's filename in the Image browser listbox, and there you are. A natural way to proceed with your familiarization with photoQuad is to try and perform some actions in the order described on this page. Try the "Image" menu for some image enhancement options (contrast, color balance etc), go to the "Quadrat" menu and try to manually define the quadrat, calibrate the image, and spawn some random points or draw a freehand region. Be patient, browse through this webpage before using photoQuad, and wait for one operation to finish before clicking another tool.
Which image formats are supported?
photoQuad supports the BMP, JPG/JPEG, PNG, and TIF/TIFF image formats.
Are there any limitations regarding image dimensions or file size?
No. The software has been designed to fully support the direct import and processing of high-resolution images, without the need to manually downsample them prior to analysis. If downsampling is nonetheless needed for some operations, photoquad either perfoms it internally, or processes the image in blocks, and always delivers back the original size. Note however that computer memory is limited, and it can always run out if you go for extremes.
Which is the typical/recommended image size?
You should consider an image with dimensions of 4000x3000 pixels with 16.000.000 colors and approximately 5 MBytes in filesize to fall within the typical operation grounds of photoQuad, when its running on an average modern computer. Of course, using images with lower resolution will only make the system lighter.
Can or will photoQuad support the *.RAW image format?
It is highly unlikely, because there is no single RAW file format. In general, every manufacturer uses a different *.RAW format, while some manufacturers even use different *.RAW formats between different camera models, with very few cases being thoroughly documented. You may however find the dcraw software useful, which is an open-source project able to read and convert several *.RAW image formats to regular *.tiff images.
Should I place my source images in a particular "work" directory?
No. photoQuad can import images from any directory.
Can I use non-English characters in image filenames or directory paths?
No. Please use English characters in directory and filenames when using photoQuad. Note that you can still import non-English images in photoQuad, but you may see some mumbo-jumbo incomprehensible characters in photoQuad's directory tree.
Can multiple images be concurrently viewed and edited in photoQuad?
No. Only a single image can be processed at a time.
Why is the image browsing listbox grayed out and non-responsive?
Because it is locked. Click the toggle button with the locker icon to unlock it, and be able to import a new image.
Why do I see a bunch of mumbo-jumbo incomprehensible characters in photoQuad's directory tree?
Because photoQuad only speaks English, and your directory or file names are in another language. Please use English characters in directory and file names when using photoQuad; note however that your images will still be fully usable.
Does photoQuad's directory tree update automatically if I plug-in a USB stick or an external drive?
No. photoQuad acquires drive letters at startup, and does not update them automatically. You must click the "Update" button which is next to the drive selection popup, or go to "File" menu -> "Update drive letters".
Does photoQuad's directory tree update automatically if directory contents are changed?
No. If you change the current directory contents (e.g. via Win Explorer) photoQuad will still list the original files; go up one directory and come back in order for the contents to update.
Can you please tell me why the behaviour described in the above 2 questions?
photoQuad's directory tree browser is completely hard-coded from scratch, avoiding any dependencies from ActiveX components or Win API base services (filesystem, device monitoring, etc). A smarter modification may be implemented in a future version. Also note that if you are running photoQuad in a virtual machine, photoQuad can only access the mapped network drives/folders, i.e. network shared drives/folders that have been assigned a letter (D:, E:, F:, etc).
Can I use photoQuad to organize or tag my images?
No. photoQuad is not an image organizer software, so it does not provide any kind of automatic directory management facilitites, nor supports image grouping using custom tags.
What's included in image enhancement operations?
A range of image processing options to correct for color, brightness or contrast imbalances in the source image.
What is an image snapshot?
This is pretty much like a "history" function, but in its manual counterpart. During image editing, the user can store a snaphot of the image's current editing state, so that several states are simultaneously available during processing. The most recent snapshot appears at the bottom of the list, and snapshots can be added or deleted at will.
Does the "grab snapshot" function apply to analysis layers also?
No. Snapshots grab the color values of the image, not the superimposed layers. The idea is that some quadrat analyses may be easier to perform over different image states.
If I switch to a particular snaphot, are analysis layers affected?
No, they are two different things.
When clicking on a snaphot, the corresponding image enhancement action is applied instantly, much faster than the initial computation. Why?
Because a snapshot is not the particular settings you used to perform an image enhancement action, but rather the resulting pixel values themselves stored in the computer's memory. Thus, photoQuad does not have to perform the computations again, it only changes the pixel values accordingly.
Does the "grab snapshot" function affect system memory?
Yes. The bigger the image, the higher the memory drain. Consider that for a high-resolution color image of 4000x3000 pixels, each color component (R,G,B) is 12000000 numbers, which have to be somehow stored in memory.
What is the "detect quadrat" process?
It is the process of marking the quadrat boundary on a digital image, in order to define the effective sampling area | ..more
So why do you call it "detect quadrat" and not "outline/define quadrat" or something along these lines?
Because photoQuad can automatically "detect" the quadrat with a single click. Manual outlining tools are also there.
Is the automatic quadrat detection applicable to any quadrat whatsoever?
No. It is an automated process, and as such, it depends on some assumptions regarding the quadrat's characteristics. The most important of those is that it expects the quadrat to have a relatively bright color relative to the rest of the image, and that it is a contiguous object. Hence a quadrat made from black PVC, or a quadrat painted with black and white stripes will not work. Please read the behind the scenes section to see why.
Can I manually define the quadrat's boundary?
Yes. There are several interactive tools to do this.
Is the quadrat saved/loaded when I save/load layers?
Yes. The quadrat boundary operates on a separate layer.
Do I have to define the quadrat prior to starting the analysis?
No. Although it surely helps to organize your analysis in logical steps, there is no particular order in which objects must be defined in photoQuad. The software updates objects and their descriptors on the fly.
Can I modify or recalibrate the quadrat during analysis?
Yes, anytime.
Can I delete the quadrat, but leave the image calibration marks in tact (or vise-versa)?
Yes, they are two different things.
What happens if I have defined/drawn several analysis objects, and I accidentaly delete the quadrat?
Nothing to worry about. Object descriptors that depend on the quadrat's effective sampling area (e.g. region or grid-cell percentage coverage) will be recalculated with reference to the whole image area. Detect a quadrat again, and things switch back.
I've spent so much time manually defining a quadrat in image A. Can I use it in image B also?
Yes, follow this procedure: (1) Save the layers from image A on disk, (2) Navigate to image B, (3) Load layers from image A and select to only import the quadrat layer. If the quadrat needs some adjustment to fit image B, right-click it, choose "Move/rotate" and perform the necessary adjustments. (4) Start your analysis of image B from this point onwards.
Can I use photoQuad to analyze non-quadrat image samples?
Yes.
What is image calibration?
Image calibration provides a pixel-to-real-distance conversion factor (i.e. the calibration factor, pixels/cm), that allows image scaling to metric units. This information can be then used throughout the analysis to convert pixel measurements performed on the image to their corresponding values in the real world | ..more
How is it done?
By placing the draggable calibration marks on two points that are a known distance apart, and entering the actual distance spanned by the points in centimeters.
Do I have to detect the quadrat before calibrating the image?
No. There is no particular order in which analysis objects must be defined.
Do I have to calibrate the image before starting the photoquadrat analysis?
No. When using photoQuad, you do not have to bother with a particular order in which analyses are performed, nor follow a strict series of steps when preparing the data. As a matter of fact, you can complete a full-blown analysis with species regions, grid cell counts, whatever, and calibrate the image right before you export the results. Makes no difference, photoQuad updates objects and recalculates their descriptors on the fly.
Can I recalibrate an image?
Yes, at any particular time during the analysis. Analysis object desctiptors are automatically recalculated accordingly.
Do image zoom/pan controls apply during calibration?
Yes. In order to properly place the calibration marks, you may want to zoom-in or pan the image accordingly, and all navigation controls work as normal, even the magnifier.
Are calibration data saved/loaded when I save/load layers?
Yes, even if no other analysis object is present in the image.
What happens if I completely forget to calibrate the image and export my analysis results?
By default, photoQuad worksheet exports contain the analysis results both in pixel units (i.e. as if the image was not calibrated) and in metric units (i.e. calibrated image). In this particular case you lose the second option, so a region's perimeter for example would only be xx [pixels], not yy [cm]. Descriptors that do not depend on image calibration (e.g. coverage) are not affected.
Note however that if you have saved your analysis layer on disk, you can import it, calibrate the image, let photoQuad automatically update objects, and re-export.
What is the species library?
The user-defined species library is a core component to photoQuad's functionality, and allows the association of various object properties to particular species. It can be an MS Excel (*.xls) or a typical comma-separated ASCII file (*.csv) | ..more
How is the species library formatted?
Read all about it here.
Is there a demo species library included in photoQuad?
Yes, both in *.xls and *.csv format; you can further use them as a template to start your own custom species library.
Does my custom species library have to be in a particular "work" directory?
No, the concept of a "work" directory does not apply to photoQuad. Files can reside anywhere on disk.
Is there a maximum number of library entries?
No, but note that if you use an MS Excel file, you are limited by the number of lines the Excel software allows.
Why do you support two different file formats?
So that MS Office is not needed in order to use photoQuad: If MS Excel is not installed on your PC, you cannot view or edit *.xls files; photoQuad however will still be able to read/write them. If you don't have MS Excel installed, you should only use the plain ASCII text (*.csv) option for your species library.
What happens if I have already defined some analysis objects (e.g. regions, random points, etc) but forgot to import a species library?
No worries. photoQuad is designed to make these things easy to forget. Try to associate an object to a species: if a library is there, things will work as normal; if no library has yet been imported, photoQuad will prompt for one or suggest to use the embedded library. The work done on analysis objects is not affected.
What happens if I enter duplicate Species or Group IDs?
You severely compromise your results, and you are up for unpredictable photoQuad behaviour. Please note that Species names and Group names are only there so that we, earthlings, can understand what's going on. photoQuad only cares for those numeric IDs, and it expects them to be unique per Species and Group category. Therefore, it is always safer to use photoQuad's interface to add/remove library entries.
Do Species or Group IDs need to be consecutive?
No, they just need to be positive integers and unique per Species and Group category. If you had a library with 4 species, their IDs could be "1, 2, 100, 3" or "1, 2, 3, 4", but not "-1, 2, -100, 3" or "1, 1, 2, 1". It's that simple.
How do I start a new species library?
You can do this in multiple ways:
Method 1: download this file (*.xls) or this one (*.csv), and use it as a template. Leave the first line untouched (Headers), delete all entries from line 2 and downwards, read the simple specifications described on this page, and start using your custom library.
Method 2: Launch photoQuad and import the embedded demo library. To do this, either press the "Load demo species library" button found on the "Library" tab, or select "Import demo library" from the image's menu. Now press the "Add/remove entries" button found on the "Library" tab. On the new window, you can find a "..Save a backup" button at the bottom-left corner. Use it to make a copy of the embedded library, and start modifying as described on Method 1 above.
Can I add more columns to my species library file (for notes, temporary entries etc)?
Yes. photoQuad only reads the first 4 columns and ignores the rest.
Are blank rows allowed in the species library file?
No. This will result to a "blank" Species name, but there will be no numeric ID for it, so photoQuad will be confused.
Can I remove the Headers from my species library file?
No.
Do I have to spell the Headers exactly as they are in the demo libraries?
No, but why would you want to change this? Please treat the species library as a sensitive system file. The whole photoquadrat analysis process can be rendered useless if the species library is messed up, so best practice is to start building your library using the demo files provided. Please avoid improvisations here.
Can I associate preview images to particular species library entries?
Yes. Read all about it here.
How can I access my species preview images?
Go to the "Library" menu, and select "Create backup of species preview images". Store them somewhere safe, and you can browse them there. Do not rename these files if you intend to re-import them to photoQuad, e.g. after a new photoQuad update installation.
What are station metadata and what do they include?
They are extra information that describes the particular sampling station, and include station name, transect number, and sampling depth. If defined, they are aytomatically attached in worksheet export filenames to facilitate file management | ..more
Is my analysis session compromised in any way if I completely ignore station metadata?
No.
How do I define them?
Go to the "File" menu and click "Station properties..", or right-click the status bar.
Do sampling station metadata automatically increment when I browse through images?
No. They are ment to change manually. It is common to randomly browse through several images before settling down to the one that will be analyzed, so an automatic system would require some "auto-increment enable/disable" options, which are easy for the user to forget and create confusion.
Can I use any station name I want?
Well, yes, but since the sampling station field is used as a suffix in exported filenames, there are some restrictions. Since a filename cannot contain any of the characters /\:*?"<>|, so does the station name. If you use any of these, they are automatically replaced with the underscore "_" character.
Can I use non-English characters for station names?
It is strongly recommended that only English characters are used, which actually applies with every work done on a PC.
Can I see an example of a valid station name?
Station names like: "my station 12", "dive site North" or "dive_siteNorth" are just perfect.
How many stations can I add/remove?
There is no limitation.
What is a layer?
Layers are commonly used in digital image processing to separate different objects, and to allow their independent editing without affecting the underlying image. The photoQuad software is built around such a layer-based environment | ..more
Which are the analysis objects that operate on separate layers?
Almost everything that you draw on the image in order to measure, calibrate or analyze it, including random points, species markers, grid cell counts, and freehand or image segmentation-based species regions, measurement tools, the quadrat boundary and the image's calibration marks.
Can I toggle a layer's visibility on/off?
Yes. Use the corresponding checkbox in photoQuad's floating GUI.
Can I delete a particular layer?
Yes. There is a small "x" button next to each layer's checkbox. Pressing it will spawn a confirmation dialog, and delete only the particular layer. As an extra precaution, the layer must be visible before photoQuad allows you to delete it.
Can I delete all layers with a single click?
Yes. Use the button with the trash bin icon in photoQuad's floating GUI.
Can I change the layer stacking order, e.g. move the species markers above the random points?
Yes. Use the buttons with the up/down arrows in photoQuad's floating GUI.
Can I save my work and continue later?
Yes. Go to the "File" menu and click "Save layers". Load them the next session and take it from there. Note that the image itself is not saved, just the layers above it.
If I load a layer file from disk, will the imported layers still function independently?
Yes, the loaded layer structure is registered in the system, and everything works as normal.
Can I save only a particular layer slot, e.g. the random points only?
No. The whole layer structure is saved, blank slots included. We'll fix this in the upcoming version, please read this section for details.
Can I load the layers from image A into image B?
Yes, but it's like wearing someone else's clothes. You'll be warm, but not look good. This does not always apply for the quadrat boundary however, so please read this section for a walkthrough.
What is a species marker?
Species markers are indicators that flag a particular image feature. They can be associated to a species library entry, and be used to obtain presence/absence or frequency of occurrence information | ..more
Are species markers automatically confined into the quadrat's active area?
No. They can be anchored or dragged around anywhere on the image.
Do species markers depend on image calibration?
No. Species markers carry no distance or area information, and therefore don't depend on calibration data.
Can I use species markers to quantify area, coverage or other related information?
No. Species markers just mark stuff, and the software simply counts and tabulates them according to the species that they have been associated with. As such, species markers only provide presence/absence or frequency of occurrence information. For coverage and related descriptors analyze the photoquadrat with species regions, random points, grid cell counts, or image segmentation regions.
How does photoQuad handle multiple marked instances of a particular species?
By providing all the information available. Both the total number of species marked, as well as the total number of individuals marked per species are readily available in the output.
Let me rephrase the above: If mark species A 5 times, and species B another 3, what's in the output?
That you have 2 unique species, their names, and their IDs. You'll also be notified that you have 5 occurancies of species A, and 3 occurancies of species B, which alltogether make 8 total occurancies. Finally, you'll get the image's metadata (filename and source path) so that you know where all of this took place.
Can I reassign a species marker during analysis?
Yes. Right-click it and select the "Assign to species".
Can I reset a species marker i.e. switch it back to unassigned?
No. Just delete it.
Do species markers update automatically when I update the species library?
No. Please read this section for details.
Is there a keyboard shortcut for entering a new species marker?
Yes. Press "c" while the main image window has focus.
What happens if I enter a species marker, but I have not yet imported a species library?
photoQuad will automatically prompt for a custom species library, or suggest to use the embedded one.
Can I toggle species markers' visibility on/off?
Yes. Use the corresponding checkbox in photoQuad's floating GUI.
Can I reconfigure the grid properties while some grid cells are already activated?
Yes, the grid can be reconfigured at anytime. Note however that active cells depend on the underlying grid, so photoQuad will spawn a question dialog asking permission to delete any active cells before reconfiguring the grid.
Can I analyze more than one species at once using grid cell counts?
Not in the current photoQuad version; currently only one species can be analyzed per grid session. We will fix this in an upcoming release, until then look here for a workaraound.
How can I delete some active grid cells?
Launch the single-cell toggle tool and click on the selected cells to deactivate them. To delete all cells, right-click any cell and select "Delete all cells".
Why does the interface become sluggish (slow) when I activate a large number of grid cells?
Please read the known limitations section. Regardless of that, you are probably using a very small elementary cell size and try to cover a very large image feature; consider increasing the cell size if this is the case, so that fewer cells are needed to cover the object.
Can I toggle the grid's visibility on/off?
Yes. Use the "Show grid" and "Show cells" checkboxes in photoQuad's floating gui to independently toggle the grid and cell visibility respectively. You can also control the visibility through the Layers tab. Please note however that only the activated cells can be controlled from there, since these are the actual analysis objects.
Can I detect/define the quadrat after creating the grid?
You can, but please don't. If you are analyzing an image that contains a quadrat frame and you want the grid to be confined within it, please detect the quadrat before spawning the grid.
What's the random point count analysis?
It is a commonly used way to statistically estimate percentage coverage of organisms from image samples. The idea is that instead of exhaustively counting each and every organism, one could superimpose on the image a number of randomly distributed points, visually identify and count the organisms beneath each point, and use these counts as a proxy of the actual population characteristics | ..more
Are random points automatically confined into the quadrat's active area?
Yes, but you have the option to disable this feature.
Do random points depend on image calibration?
No. Random points carry no distance or area information, and therefore don't depend on calibration data.
Can I re-assign one or multiple random points during analysis?
Yes. Select them, right-click, select "Assign to species" from the context menu, and choose the appropriate library entry from this interface.
Can I customize the color of assigned points, so that it differs among species?
No. In the current implementation, two categories are only separately colored: "unassigned" and "assigned" points. You cannot have separate coloring within these categories. We'll fix that in an upcoming version.
Can I reset a random point i.e. switch it back to unassigned?
Yes. Please read this section.
What happens if I try to assign some random points, but I have not yet imported a species library?
photoQuad will automatically prompt for a custom species library, or suggest to use the embedded one.
Can I toggle random points' visibility on/off?
Yes. Use the corresponding checkbox in photoQuad's floating GUI.
When I use the "Stratified random" or "Uniform" distribution, I sometimes see more than one point in each stratification sub-cell. Why?
This is how the stratification algorithm works. If you ask for N points total to spawn, the software tries to stratify the spawn canvas in a grid of n rows by n columns, i.e. n2 sub-cells. To do that, it looks for an n value that is the largest square root that is equal to or smaller than N. For example, if N=100, cells will be 10-by-10 and each cell is populated with 1 point. if N=36, cells will be 6-by-6 and each cell is populated with 1 point. But what if N=63? Cells will be 7-by-7 (=49), each cell will be populated with 1 point, and the remaining 14 points are randomly spawned anywhere on the image; total is 63, but some stratification cells will have more than one point within them.
What's the species regions analysis?
Species region analysis refers to the drawing of an outline around a specific image feature, its association to a particular species library entry, and the subsequent extraction of region descriptors regarding its area, coverage, perimeter or other morphological information | ..more
What's the difference between a region of interest (ROI) and a species region?
A species region is a ROI that has been associated to a species. Please read this section for details.
Are ROIs included in the summary report and worksheet export?
No. Only assigned species regions are considered.
Can I draw a ROI without having to import a species library?
Yes. A species library is only needed in order to assign a ROI to a species.
What happens if I try to assign a ROI, but I have not yet imported a species library?
photoQuad will automatically prompt for a custom species library, or suggest to use the embedded one.
Can I re-assign a species region during analysis?
Yes. Right-click it and select the "Re-assign to Species".
Can I reset a species region i.e. switch it back to unassigned?
Yes. Right-click it and select "Unassign and revert to ROI".
Can I select and assign multiple regions at once?
No. But you can try this method that works almost as fast: Start by drawing the necessary ROIs. Right-click one of them, select "Assign to species", and enable the "on top" checkbox in the region assignment window. Now right-click and assign ROIs consecutively.
Can I define species regions using photoQuad's image segmentation algorithm?
Yes. Use image segmentation to automatically partition the image into segments. Select the segments you prefer, and convert them to ROIs. From that point, everything works as described on this page.
Can I modify the outline of a ROI or species region during analysis?
Yes. Right-click it and select the "Break to nodes and Edit" option.
If I modify the outline of a species region, its characteristics obviously change. Do I have to force photoQuad to update the region's descriptors?
No. photoQuad automatically updates region descriptors each time the quadrat boundary, the calibration data or the region itself is modified. No matter when you request for a summary report and worksheet export, you will always get the updated information.
Can I toggle ROIs or species regions visibility on/off?
Yes. Use the corresponding checkbox in photoQuad's floating GUI.
When I right-click a region, there is an interesting "Add pocket region" option. What's this and why haven't you mentioned anything about it in the main text above?
This feature is designed to allow for internal holes inside regions, and the subsequent calculation of appropriate descriptors. The work is still under progress and will be fully functional and documented in the upcoming photoQuad version. Currently, only the graphical part is completed i.e. you can add as many pocket regions as you want, but they are ignored when parent region descriptors are calculated.
What is image segmentation?
Image segmentation refers to the partitioning of an image into multiple sets of pixels (segments) that share some common characteristics such as color or intensity. The output is a segmentation map, i.e. an alternative representation of the source image that is easier and considerably faster to analyze | ..more
What's it good for?
It is a fast, automatic, user-independent method to rapidly define Species regions.
Is there anything I need to know before working with image segmentation?
Yes. Please have a look at the Species regions page, so that you are familiar with Regions Of Interest (ROIs) and Species regions.
I know what ROIs and Species regions are, but I am still confused: what is a segment map, an active segment, and a selected segment?
These terms are documented in this walkthrough.
Can other analysis objects be present on the image when working with segments?
Yes. You can simultaneously work with any analysis object, e.g. random points, grid cell counts, species markers, measurement tools, whatever, they all operate on different layers. If the display gets confusing, just toggle some layers invisible.
Are the various image navigation tools available during segment-based processing (e.g. the magnifier, interactive zoom/pan etc)?
Yes. To our surpise also, all these work as normal...
Can I segment the image without having to import a species library?
Yes. A species library is only needed in order to assign Regions Of Interest (ROIs) to species.
Why do you call it "multi-scale" image segmentation?
Because the image is segmented into four different scales from coarse to fine detail, facilitating the automatic location of features and boundaries at different levels of detail.
Can segments from different scales be combined to produce a single ROI?
Yes, that's the point of having multiple scales.
Can I customize the level of detail produced by each segmentation scale?
In a strict sense, no. These settings are hard-coded and refined to produce optimum results in a wide range of scenarios.
But there is a workaround: you can increase the produced detail by lowering (or even unchecking) the "minimum segmentation threshold" checkbox. Please refer to this walkthrough for taking the most out of photoQuad's segment abilities.
Can ROIs produced from image segments be re-attached to the segment map?
No. The segment map provides the background for ROIs to be rapidly defined. Converting a particular group of segments into a ROI does not affect the segment map underneath. Just delete a ROI if you don't need it.
When I convert segments to Species regions, do I have to force photoQuad to calculate or update the region's descriptors?
No. This takes place automatically in the background. Even better, photoQuad automatically updates region descriptors each time the quadrat boundary, the calibration data or the region itself is modified. No matter when you request for a summary report and worksheet export, you will always get the updated information.
Can I save the segmentation map so that I can reuse it in another session?
No. The segment map cannot be saved; you can only save the ROIs and Species regions layers produced. Note however that since segmentation settings are hard-coded in the software, multiple segmentation attempts will produce identical results for a particular image. So, to continue work from a previous session, load the previous layers, segment the image again, and take it from there.
Can I modify the segment map?
No, but you can modify the ROIs and Species regions produced.
Can segments be confined within the quadrat's boundary?
Yes. Enable the "Crop to quadrat" checkbox in photoQuad's floating GUI. This not only looks better, but also saves system resources because image segmentation is demanding in computer memory.
I understand that segments can be optionally allowed to have internal holes, but that doesn't seem to make any difference in the output Species region descriptors. Why?
Please read the answer to the this question in the Species regions FAQs. The work with parent and child regions is still under progress, and currently the software simply ignores inner holes when calculating descriptors. Whether you use them or not, results will be identical as if holes where not there.
Can I make all segmentation objects temporarily dissapear, so that I can work on another analysis?
Yes. You must hide the segmentation map and disable the segment selection mouse hover function. To do this, go to photoQuad's floating GUI, disable the "Show segment map" and "Show boundaries" checkboxes, and toggle the Mouse hover button to "Off". All segmentation info is thereby hidden, but you can still come back to it and continue your work.
How are photoQuad exports formatted?
They are comma-separated value (*.csv) plain ASCII files.
I have worked numerous times with comma-separated files. Is there anything special here I don't know?
No.
What is the ASCII format and why go for it?
The ASCII text format is a nice way to disseminate data because it is the absolute lowest common denominator of formats. This means that even a 20 year old computer can read ASCII data without depending on any custom or proprietary software. ASCII data can be created by photoQuad running MS Windows, analyzed on a unix system, moved to or viewed on a computer made in the 90's, and still be equally usable in the future; they occupy small disk space and, if properly formatted when created, they are ready for statistics. Even if everything else fails, you can easily write your own computer program to read them. These are some very good reasons to prefer this format, and explains why ASCII is generally the format of choice in scientific exports.
How do I convert photoQuad exports into spreadsheet format for statistics?
You don't, it happens automatically when you open them with a spreadsheet software, e.g. MS Excel.
MS Excel, general-purpose spreadsheet programs, and all serious statistical packages have built-in functionalities for "converting" ASCII files into spreadsheets. This is not actually a data conversion, but rather a data rearrangement: to put the data into a spreadsheet, the software needs to know which are the rows and which are the columns. Although no global specification exists, the widely accepted default is the comma-separated format: lines in the ASCII text file represent rows in a spreadsheet, commas (,) separate the columns, dots (.) denote the numeric decimals. This is why photoQuad's ASCII analysis exports are "comma-separated value" (*.csv) files:
If I double-click a photoQuad export file, will it open in a text editor or MS Excel?
In Excel, but it depends on your computer's custom configuration:
If you have MS Office installed, Excel automatically associates itself with *.csv files, and you see them in Explorer with an Excel icon. In this case, double-clicking a *.csv file will automatically open it in Excel. You can always override this behaviour (as with any file on your PC), and associate the *.csv file extension with another software.
If no spreadsheet or statistical processing software is installed on your computer, you would probably not be reading this page... Anyway, in this case *.csv files will open in your default text editor.
Should I do statistics with *.csv files or first convert them to Excel format?
Whatever, but keep a backup of the original file.
What is this "Export to new file" and "Append to existing file" option?
These options appear in all of photoQuad's export interfaces. Here's why:
In a real-world situation, one would normally want to analyze a sequence of image samples, measure whatever it is to be measured, and end up with a single output file that contains the appropriate information for this particular session. This means that the output file must contain the headers in the first row, and then have the results tabulated per image; something like the image below:
photoQuad makes sure that the "we want this to happen" case automatically happens, so that analysis exports are ready for statistics. Instead of exporting each analysis separately per image and then having to manualy merge the files, the options provided do that automatically:
Use this button the first time you export an analysis, e.g. for Image_1.
This way, photoQuad exports both headers and descriptors.
Use this button to append (attach) new exports to the initial file e.g. for Image_2, Image_3, Image_4, etc. This way, photoQuad exports only descriptors.
Note: When using the "Append to existing file" option, you get a funny question dialog with a message like this one: "This bla_bla_bla.csv file already exists. Do you want to replace it?". This is due to the MS operating system itself, just ignore it (...sigh). Choosing the append option does not delete the file, it just appends the new data.
Warning: This one is real, and it's serious. If you choose the "Export to new file" and select a pre-existing export file, it will be overwritten. That's why we placed the "Export" and "Append" buttons so far away from each other. A safe practice is to keep your completed/pre-existing original exports in directory A, and use a temporary directory B for building a new export session; when done, move the completed file to the "safe" directory A.
Important !
When exporting your data, make sure that the target file is not simultaneously opened in Excel or in another application.
Excel takes hold of the file and prevents other applications from having write-access to it, so photoQuad will not be able to export the requested data. If this happens, you will receive a message saying so. Please close the target file from Excel and repeat the export.
I have appended some results by mistake. How do I remove them?
You will have to do this manually. The data to be removed are at the end of the export file: open the file with a text editor (or MS Excel for if you prefer), delete the appropriate lines, press save, and close the file. If you remove some data lines from the middle of an export file, make sure you leave no blank lines.
Can I use non-English characters in filenames, directory paths, etc?
Please don't. It is strongly recommended that only English characters are used when working with photoQuad.
