Video capture:
Video editing: Testing and Organizing: Schematicoverview figureof the main steps
STAGE 1: VIDEO CAPTURE
A. Initial preparations for video capture:
In the initialisation step, a few settings need to be changed or checked in the camera, computer and capture software. During installation of the card and its software, a folder named "capture" was automatically created on the top level of the hard drive for receiving all captured clips. If it is missing, reinstall miroVideo Capture. To save all edited and finalised clips, it is advisable to add another folder, named e.g. "Edited clips".
The program itself needs to be adjusted too. Start miroVideo Capture and choose Advanced in the "Mode" page. Switch to the "Settings" page and set the Data rate to 4000 kbps. Higher values will lead to excessive pixel redundancy, while progressively lower values will reduce image quality. In the "Image settings" box on the same page, move the sliding button of the sharpness icon to the rightmost setting.
Switch to the "Projects" page and click on the Create new project button. This will create a new folder in the "capture" folder. Change the name from "Unnamed" to an appropriate specimen code, species or genus name, etc. In the same page, unmark the "Capture audio" check box, and mark the "Full" bullet and the "TV cropping" check box for frame resolution. Select the video standard as appropriate for the video camera (in our case: PAL) and set the "Frames/Sec" drop-down menu to 25 frames per second (fps).
Switch to the "Record" page in miroVideo Capture, connect the camera
to the power grid, switch on the light source of the LM, and channel enough
light to the camera adapter to obtain a moderately bright background in
the video display of the "Record" page. Use the camera setup buttons to
change the following options in the camera setup screen. In the VIDEO ADJUST
menu set ENHANCE to 5 for maximal sharpness. In the MODE SELECT menu set
SHUTTER to MANU (1/120), set W.BAL to MANU, and adjust the white balance
by eye.
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Place a specimen on the microscope stage, switch to an appropriate objective,
i.e. 40x-100x, and select the part of the specimen that needs to be recorded.
Channel all light from the objective to the camera adapter. The "Record"
Page in miroVideo provides a real-time display window for the camera output,
as well as a recording button and a text box for naming each clip. Always
name the clip unambiguously according to the selected slide and specimen,
to avoid subsequent confusion (especially if you are planning to capture
structures from different specimens in the same slide). Using the microscope
stage controls, position the selected part of the specimen in the video
window, and swivel the camera adapter until the main axis of the selected
structure or body part lies horizontal in the video window (this will simplify
cropping to remove background redundancy „ see below).
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Turn up the fine focus of the microscope (i.e. lower the stage) until the specimen is just out of focus. Click on the recording button, wait a fraction of a second (actual recording starts with a delay of approximately one quarter of a second) and then turn down the fine focus in one continuous movement until the specimen is just out of focus on its other side, and then stop recording. Ideally, the entire recording should take you between 1 and 2 seconds: at 25 fps you will obtain a final clip of at least 25 frames/~4 Mb and no more than 50 frames/~8 Mb, thus avoiding excess storage in the "capture" folder on the hard disk without compromising on the recorded number of focusing levels.
After each recording, switch to the "Clips" page in miroVideo Capture
to check the result. Verify that it includes focusing levels of the cuticular
surface (if these are missing, then you moved focus too soon after clicking
the record button) and that the number of frames and Mb is neither too
small nor excessively large. If the clip is not satisfactory, delete it
and capture the selected part again. If the clip is acceptable, move on
to another part of the same specimen, or position another specimen, and
repeat the procedure until you have captured all the required structures
and specimens. When finished, close miroVideo Capture and all other programs.
You are now ready for clip editing.
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STAGE 2: VIDEO EDITING
A. Editing out duration redundancy
Open Adobe Premiere. Keep in mind that this program utilises most of the available memory, so do not run any other software in the background. Also, take note that Premiere is a virtual video studio intended for pasting and modifying source clips into a complete video sequence. While it can be considered to be the video equivalent of still image editing software, it also includes many effects and options that are not relevant to still images, and uses video editing jargon that may sometimes seem at odds with terminology used in still image editors.
For example, the program works with so-called projects which represent complete video sequences in the making - and which are not always directly relevant to our purposes, since we are primarily interested in the editing of individual clips. Thus, the "Open" and "Save" functions apply to entire projects, but not to clips, and need not be used for most of the applications described below. Nevertheless, when opening Premiere one must first specify project settings before importing clips for editing: in the "New Project Settings" window, choose the subheading "General Settings" and select "DC30 Editing Mode", "25" as timebase, "25 fps Timecode" for time display. Click "Ok".
Next, make sure the "Project" and "Timeline" windows are open (if not, open them via the the "Window" menu in the menu bar). Import one or more of the clips that require editing, by selecting the cascading menus "File" ® "Import" ® "Fileƒ" and browsing for the desired clips in the "capture" folder. These clips will then appear as a list in the "Project" window. Note that the "Duration" column in this window (and in others that will appear later) specifies the length of each clip as minutes : seconds : frames, and not as minutes : seconds : hundredths of seconds. In other words, a duration of 00:02:04 at 25 fps corresponds to 54 frames, not 51.
In the "Project" window, move the cursor to the little film icon on the left of the name of the highlighted clip. Grab and drag this icon into track "Video 1A" of the "Timeline" window, making sure that you drop it on the leftmost side of this track. Check the settings of this window. The leftmost check box of track 1A should display an eye icon (if it doesnÍt, click this check box to enable real-time display of the track in other windows). The second drop-down menu in the lower left corner of the "Timeline" window is preferably set to a value of "12 frames". Double-click on the clip in track 1A.
After a few seconds, the "Monitor" window will open, showing you two video display windows with a series of controls. The left display shows the selected source clip, while the right display shows the edited and assembled video sequence. For our purposes, true sequences are usually not assembled, and the right display is used at most to verify the operations performed on the source clip in the left display.
The "Monitor" window can be used as follows to remove duration redundancy.
After opening the source clip in this window, click on the right arrow
until you reach the first frame with structures that are truly in focus
(e.g. setae or other cuticular surface features). In the controls at the
bottom of the left display, click on the "Mark In" button, and then click
on "Apply" above the left display. Scrub to the end of the clip, and then
click the left arrow until you reach the last frame with any focused structure.
Often, this side of the body is much fuzzier, and for bigger specimens
it may be pointless to try and focus on the cuticular surface. When you
are satisfied with your choice of the last informative frame, click the
"Mark Out" button and then the "Apply" button. To verify the proper operation
of these functions, play the shortened clip in the right display by clicking
on the play button below it. If all is well (i.e. you have not inadvertently
removed informative frames), take note of the number of frames and move
on to the next step in editing.
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B. Annotating frames with text, scale bars and/or arrows
After resizing the clip, it is possible to add various graphical objects
to one or more frames. Space does not permit us to describe here the complete
procedure for doing so, as it involves a considerable number of operations
in several windows. In brief, titling objects such as text, scale bars,
pointers and other graphics are constructed in separate Title windows,
using one of the frames of the clip in the Monitor window as reference
background for positioning. The resulting titles/objects are then pasted
into separate tracks in the Timeline window, with a transparent background
or "Matte", and over the appropriate range of frames so as to match the
frames in the clip that need titling. By choosing different ranges of frames
for different titles, it is possible to effectively label different structures
occurring at various levels of focus (see example).
Title tracks are merged with the clip in the next step.
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C. Removing other redundancy types through editing and compression
Select the menu cascade "File" > "Export" > "Movieƒ", and click on "settings" to access a series of windows that will allow you to remove or minimize background, frame, pixel and resolution redundancy. In the "Export Movie Settings" menu, first select "QuickTime" as File Type and uncheck the "Save Audio" box.
Then select the "Video settings" subheading to choose a codec and to optimize the frame rate of the source clip. For the time being, the most appropriate choice of compressor is "Cinepak", since it is available in both recent and older implementations of QuickTime and Windows Media Player, and reduces file size three- to four-fold without discernible loss of quality. Note that more recent codecs exist (such as "Sorenson"), which will reduce file size more, but these codecs are not included in older versions of movie playback programs, and the resulting files may therefore not play on the computers of some potential users.
Next, set the frame rate to a value that will result in a finished clip with about 25-30 frames (e.g. if the source clip contains 41 frames, set the frame rate to 15 fps to produce a finished clip with 24 frames). Make sure the "Depths" menu is set to millions, and "Quality" to 100%. "Frame Size" should be 720 by 540 or 360 by 270, depending on the appropriate resolution of the final application (the second setting reduces file size and image area by a further 75%). Do not select the "Recompress" option.
In the subheading of this window, select "Special Processing" to address background redundancy. Click on "Modify" to open the "Special Processing" window, and use the rectangle controls in the resulting video display to crop background areas present throughout the clip. After selecting the rectangle, scrub forwards and backwards to verify that you are not about to crop informative parts of any frames. Compare the reported coordinates of the cropping rectangle with the reported size, to check for a possible miscalculation bug, and if necessary correct only the coordinates but not the rectangle (see discussion). Leave "Gamma" at 1.0 and do not select any other options in this window.
Click "Ok" twice to return to the "Export Movie" window, select your folder for exported files (make a subfolder if necessary), type the name of the finished clip and click "Save". You can use the same name for the finished clip as that of the source clip, (the name of the latter is displayed in the "Monitor" window), because the two versions are in different formats and will have different extensions (.AVI for the source, .MOV for the finished clip). With the Cinepak codec, it takes our system between 1 and 4 minutes to compress and export a 25-frame finished clip, depending on the chosen degree of cropping and resolution. The codec is asymmetrical in that decompression is much faster. After finishing compression, Premiere opens a window that displays the finished clip and allows you to scrub through it with playback controls. Check the finished clip, and close this window. If not satisfied, return to one of the earlier steps and repeat the editing procedure as appropriate.
About 10-20% further reduction in file size can be obtained by applying generic file compression, such as the ZIP format on PC implemented in PKZip or WinZip. In many cases, however, this extra step may not be worth the additional time required, and it will prevent the VCE clips from being playable until they are "unzipped" again.
A. Testing the clips
Open the finished clip in QuickTime or Windows Media Player to verify that it works properly. Both programs provide a display window with a sliding knob for scrubbing through the clip. For display purposes, QuickTime is slightly more versatile in that it allows more than one clip to be opened, using multiple display windows. Also, in order to see frame by frame it is possible to move backwards and forwards through the clip using the left and right arrow keys. Media Player does not have these options, but instead it includes a zoom function which allows the clip to be displayed at half resolution. This is useful to compare the image quality of half versus full resolution clips, so as to assess whether the clip could be exported at half resolution from Premiere in order to reduce file size. If you have both Macintosh and PC-compatible computers, try the clips on both platforms.
If you have a series of clips showing different parts of the same nematode, you make them accessible to others by constructing an image map inside a web page. See vCenema Vol. 1 for some examples of the result. Creating an image map requires some knowledge of HTML, the code used for writing web pages. Click here or here for two links to online HTML manuals.
The rather laborious way we do it, is by first capturing a low-magnification clip of the entire nematode, and then exporting the single frame with best overall focus to a TIFF image. Next, we open this TIFF image in a vector-based image editor (such as CorelDraw or Adobe Illustrator) to add boxes and other graphics that will demarcate clickable areas in the image map. We then take the file into a pixel-based image editor (e.g. Corel Photopaint or Adobe Photoshop), and open the navigation/info windows while moving the cursor over the image, to read the coordinates of the clickable areas. We enter these coordinates into the HTML source text of a web page with the relevant code for a functioning image map. Finally, we export the overview image to a JPEG format file (with no or minimal compression), and transfer the web page, the overview image and all clips to their final destination (web server or CD-ROM).
Paul De Ley & Wim Bert - August 1st 2002