AutoMatch Quickstart

This assumes that you have some basic familiarity with the idea of image mosaicking. It also assumes that you have
¥ a video camera attached to a microscope
¥ a monitor larger than 640x480 (though a 640x480 will do, but I really don't recommend itÉ)
¥ a video/frame grabber card that is supported by NIH Image (or an AV PowerMac).

(1)	AutoMatch needs NIH Image v1.60 or later to run. NIH Image is in the public domain, you can get a copy via FTP from zippy.nih.gov/pub/nih-image/ or on the web from http://rsb.info.nih.gov/nih-image/.

(2)	Move the folder "AM Prefs Ä" into your preferences folder (You might like to keep a backup copy in your AutoMatch folder).
¥	"AM Prefs Ä" must be directly within the preferences folder of your system folder, not in a subfolder within the preferences folder.
¥ "AM Prefs Ä" must not be renamed (i.e. don't put something like "AM Prefs Ä copy" into your prefs folder).

(3)	Launch NIH Image and set the "Video controls" in NIH Image.

(4)	Choose "Load MacrosÉ" from the "Special" menu of NIH Image, or press cmd-9, to load AutoMatch into NIH Image.

(5)	Press F1, or choose "AutoMatch" from the "Special" menu, to start AutoMatch.
The AutoMatch Main Window (from now on called "Image Manager") will appear.

(6)	Set the preferences for AutoMatch. Most important, set the "screen sizeÉ" according to your monitor dimensions. For now, you can leave the other prefs as they are by default.

CAVEAT: The preferences dialog boxes have "cancel" buttons
 - NEVER HIT CANCEL!! Rather, to leave the dialog without changing anything, hit "OK"!!! Cancel aborts the macro execution, leaving a lot of internal files open in NIH Image. If you should have hit "cancel" by accident - no problem, just don't panic. Rather, type alt-cmd-W to close all open windows and always say "NO" if NIH Image asks whether you'd like to save changes to all those weird internal files - or, even simpler, use the mini-macro "Oh bugger, it crashed!!!" in the special menu of NIH Image.

There comes a third dialog - 
¥ if you don't have this funny black upper and left margin if you display live video on your Mac, don't think about it, set it to zero & say OK.
¥ Otherwise (you have an AV Mac, I reckon  :), spezify the height of the upper margin in pixels (we don't need to know the left margin).
AUTOMATED MOSAICKING WILL FAIL IF YOU SPECIFY A VALUE THAT IS SMALLER THAN THE HEIGHT OF THIS BLACK MARGIN!!!!

(6)	Click "Acquire" to enter the image acquisition mode. A window should appear with various buttons, only two of them being enabled: "Abort Acquisition" and "New Background".

(7)	Click the "New Background" button to acquire a background correction frame. A  "Camera (live)" window will show up.
¥ FIRST, move the microscope stage so that your specimen shows up in the live window and adjust the illumination settings on your microscope for optimum image contrast (no brightness overdrive, proper setting of the diaphragm etc.).
¥ THEN move the stage so that a clean, empty area of the slide appears in the live window (or replace the slide with an empty one) and hold down the mouse until you hear the system beep.
Never acquire the background frame without a slide on the stage!

(8) Click "Next frame" to acquire the first of a series of overlapping frames from the specimen; the camera window changes to "Camera (live)" again. Move the stage to the region within your specimen where you want to start. Mouseclick to acquire the frame. A "previously captured" window will show up left to the "Camera" window.

(9) Click "Next Frame" again to get live video again. Shift the slide. There should be an overlap of approximately 10% with the "previously captured" frame. Check overlap by comparing the "Camera (Live)" and "previously captured" windows. To capture, push mouse button till you hear the system beep.

(10)	Repeat step 9 until you have acquired enough frames to cover the region of interest within your specimen (or the entire specimen) - i.e. all frames that you want to be mosaicked in one single compound image.
¥ Every frame needs to overlap with the previous one. AutoMatch will not look for overlaps between, say, frame 3 and 11 of a compound image.
¥ You can acquire a new background correction frame any time (but you will lose the "previously captured" window, so using a blank slide without moving the stage is a good idea).

(11)
¥ If you want to acquire another image (e.g., the next section within a series, or another region within the same specimen which you want to mosaic as a separate compound image), click "New Image" and proceed with (8).
¥ To exit the acquisition mode and return to the Image Manager main window, click "Finish Acquisition".

(12)	The Image Manager should now show a list of all images (compound images, not frames!) acquired so far, e.g. "MySection 001", "MySection 002" etc.

(13)	With the mouse, select one, some, or all compound images for mosaicking. Click "Match" to start the FFT/cross correlation matching process. Calculating the matches between the acquired frames will take several minutes for each compound image, so please be patient. If you should have acquired several hundreds of frames, it is a good idea to run the matching over night - but here we assume you have captured only some ten or twenty frames so a couple of minutes will do.

(14)	As soon as the Image Manager shows up again, you will find a tick mark on the left of every item that you had passed through the matching. These images are now ready for being reassembled.

Click "Build" to build the selected compound images.

(15) Click "Exit Image Manager" to return to NIH Image and see the result (or perform further processing in NIH Image).

¥ As a backup, the images are kept in the Image Manager item list (check by entering AutoMatch again - the images you have just built are still listed and can be rebuilt any time).
To get rid of them, select them and click "Dispose".