Fixtures
Fixtures are configuration-files stored in the Scan-o-Matic configurations data folder. They inform Scan-o-Matic about what to expect to find in an image and where. They are used to automate the analysis procedure.
For those interested, the files are stored at:
$HOME/.scan-o-matic/config/fixtures/
This is the procedure to manufacture the fixture. Fixtures can also be ordered from the following distributors:
Using a over-head sheet or similarly transparent print target, print the orientation marker. It is important that they get the right size:
Orientation Marker (svg) | Orientation Marker (png, print with 600dpi) | Orientation Marker (png, print with 150dpi)
We order our grayscales from Silverfast, make sure they are 35mm transparent scanner calibration targets.
Because this is the only available grayscale that comes preconfigured with Scan-o-Matic, we recommend you consider it.
If you wish to use another, please carefully read about adding new grayscale types first.
Here follows a design specification for the fixtures we use:
Place three markers. One in the cross between the plates and one on each side of the grayscale are. The further apart these to latter are, the better but the must be well inside the image. If they are close the the image border, errors can occur if placement of fixture in scanner isn't done with care.
Make sure the markers are correctly rotated. The program's fidelity in detecting them decreases if rotated.
Avoid rotating like this:
Creating a fixture is a two-part procedure. As a first step the path to a scanned image (using the intended scanner at the correct settings) with the fixture in it, a name for the fixture and the number of fixture position and orientation markers included on the fixture (typically 3):
Upon submitting it may take a little while for the server to analyse the fixture. But as soon as it is done you should see the selected image with the orientation markers correctly identified with a superimposed circle and 'X'.
First, select the type of calibration strip used in the drop-down below the image.
Second, mark the area that holds the grayscale calibration strip. Marking is done by click-dragging the mouse to indicate the relevant area rectangle. There is an interactive visualisation of the area being created as you do this. Once you release the mouse, Scan-o-Matic will try to find a grayscale in the area if the grayscale has yet to be detected. If successful, you will see the area marked with a 'G' and a plot indicating the analysed grayscale.
If you are unhappy with any area, you can just click inside it to remove it.
Now, mark out the plates in the fixture. The plates should have some margin to the actual colonies, but it's typically not a problem including the plastic border and a little more (if you want). The numbers will rearrange themselves according to an internal logic that ensures all fixtures have the same plate order.
NOTE: It is good practice to leave some distance between the plate marking borders and the image border in case the scanner causes an offset in where the image starts image to image.
When done with the plates. Just press save and that's it.
Simply select a fixture from the drop-down.
This will take you past the first step of fixture creation into the second part where plates and grayscale are marked.
Select a fixture as you would when updating it and press delete.
When deleting fixtures, they are actually not deleted, but their config-files renamed. So just head into $HOME/.scan-o-matic/config/fixutres/ and find the file with the matching name (files use underscore instead of space) and rename it to fit the pattern of the other fixtures in that folder.