1. Walk-throughs of tomographic z-slices to help with Sterecon tracing.

2. Animation of aligned tilt-series images to evaluate alignment quality.

Preferred creation software: Moviemaker_old. The current SGI movie maker software (Moviemaker), does not provide for selection of a series of individual image files.

Input file format: SGI(.rgb).

Preferred player software: Movieplayer_old. The current SGI movie player software (Movieplayer), does not provide frame numbers, which are needed to identify z-slices or tilt image numbers.

Quick-time

Preferred use:

1. Stand-alone movies to be played on a PC or sent to colleagues.

2. Movies to be transferred to videotape.

3. Movies to be included on webpages.

Preferred creation software: Adobe Premiere.

Input file format: Non-compressed. TIFF preferred.

Preferred player software: Quick-Time Pro, the only player which allows frame-by-frame advance, forward or backwards.

AVI

Preferred use: Movies to be included in PowerPoint presentations.

Preferred creation software: Adobe Premiere.

Input file format: Non-compressed. TIFF preferred.

Preferred player software: Works with most, if codec is one of the common ones.

Image-series movies

Collecting images for slice walk-through animations from tomographic volumes .

For SGI movies, pick slices along desired axis and make -.rgb images using SPIDER procedure file b01.dat . Then use movieplayer_old to make the movie.

input file	(e.g.) vol001.dat [tomographic volume]
output files	(e.g.) sli***.rgb [slice images in .rgb format]

For presentation movies, pick slices from a volume and make a series of TIFF images using b02.dat. Modify the procedure file as appropriate to make a series of x, y, or z slices. Alternatively, the SPIDER command CP TO TIFF can be used to make z-slice series directly (but will not make x or y slices). Then use Adobe Premiere to make the movie.

input file	(e.g.) vol001.dat [tomographic volume]
output files	(e.g.) sli***.tif [slice images in .tif format]

Collecting images for tilt-series animations to check alignment and for presentation of projection images

For SGI movies, convert SPIDER images to SGI using b03.dat, then use moviemaker_old.

For presentation, convert SPIDER images to TIFF using b04.dat, then use Adobe Premiere.

Animations from surface models using Iris Explorer

1. Use the map exp4_movie.map, available from here. The map must be copied into your working directory. This map is used with IRIS explorer 4.0 to make collections of tilted views around a defined axis.

2. Start explorer by typing explorer4

3. In the Librarian box, select File > Open, click on exp4_movie.map, then OK. This will open the needed modules.

4. The default image size will be 650x650. If you want a different size, you can use the mouse to change the size of the render window. If you want to specify the image size, you will have to edit the file exp4_movie.map. To do this, look for the following block:

(@4 =cxNRPanel [1]

{ (Title "Render")

(MaxiSize =cxWidgetSize

{ (width 712)

(height 712)

Note that a value of 712 in the example gives an image dimension of 650 pixels. Thus, replace 712 with the desired value, plus 62.

5. Click OK in the ReadGeom Module Alert box.

6. Resize the Map Editor to uncover the other modules and keep it out of the way of the Render window.

7. Type in the desired output file prefix in place of "junk" in the WriteImg box. Do not alter anything except the letters "junk". The default file format is set to TIFF.

8. In the TransformGeom box, select the axis you want to rotate about (x, y, or z). It is possible to rotate about an arbitrary axis by moving the camera position using the thumbwheels on the Render box to get the desired starting view,then using the TransformGeom box to select an axis relative to the original ("home") view.

9. Type in the desired starting, ending, and increment values in the For box: For each value, click on the place "0.00" initially appears. A white box will appear around the number, and a typing cursor will appear.

10. Type in the model file name in the ReadGeom box (which initially has ".geo").

11. When the model is displayed in the Render window, select the desired perspective and transparency-rendering options. Normally, perspective should be off. Under Viewing you should normally select Delayed Blended Transparency for transparent objects. Also under Viewing, you may want to turn on Anti-aliasing. Although anti-aliasing slows down the rendering quite a bit, it gives the best possible result (smooth, not stepped, edges).

12. Finally, enable the For module to start the animation run. It is important to do this last, since the animation procedure might start prematurely otherwise. To enable a module, left-click on the module in the Map Editor to select the module, then right click in the upper portion of the box and select Enable.

13. After the animation run is finished, be sure to disable the For box before setting up a new animation run.

Extracting images from SGI movies for Adobe Premeiere

1. Open movie in moviemaker_old: Type moviemaker_old [filename] , or start the application then use "File > Open".

2. Select File > Export > Collection of Images. Specify a file name in the box. Just type two or three letters, with no following numbers or extension. The files will have a serially-numbered extension.

3. Note the size of the frames. Use imgsize [filename] .

4. Convert the images to TIFF using imgcopy [filename] . This flips the image around the horizontal axis, so the option -ctl [filename] is needed. Use the SPIDER procedure file b05.dat.

5. Copy the files to the hard disk on the PC. The application WS-FTP on the PC is the most convenient method. Premiere may not open all the files if they are on a cross-mounted SGI disk.

Use of moviemaker_old for SGI movies

1. Start the application by typing moviemaker_old

2. Select File > Insert.

3. Highlight all the desired files.

4. Wait until the files have been loaded (thumbnails of the frames will appear).

5. Select Options > Optimize Movie .

6. Quit application when optimization is complete.

NOTE: The first movie made will be automatically named "untitled.movie.0", and subsequent movies in the same directory will have file names incremented starting from 0. Rename the movie files as desired. You may use the extension ".mov", but be aware that this extension is automatically interpreted by some PC systems as a QuickTime or AVI movie.

Use of Abode Premiere for presentation or distribution movies

Step1. Start the application. Premiere only works on the PC.

Step2. The New Project Settings box will appear. There are five screens in this box. You can access them by the pull-down menu or by using the Prev and Next buttons.

General Settings:

Editing mode: Video for Windows

Timebase: 30

Time Display: 30 fps Non Drop-Frame Timecode

Video Settings:

Compressor: None

Depth: Millions

Frame Size: (Put in original size. Do not check 4:2 Aspect)

Frame Rate: 30

Audio Settings

(not used)

Keyframe and Rendering Options:

Fields settings: No Fields

Check Optimize stills

Capture Settings:

(not used)

Step 3. When your settings are completed, click on OK.

Step 4. Import images:

1. Select File > Import > File

2. The Import box will open.

3. Set file type to TIFF using the pull-down menu.

4. Browse to the directory where the files are.

5. Select the first file of the series.

6. Check Numbered Stills, again select the first file.

7. Click on Open. The clip will appear in the list in the Project box.

(Note: the files have to be on the local disk, not on a cross-mounted SGI disk

Step 5. Load the clip: Left-click on the clip in the Project box. When you click under the Item column, a hand will appear. Keep the mouse button down and drag the clip to track Video 1A in the Timeline box.

Step 6. Play the clip in the Monitor box: Select the clip in the Timeline box by left-clicking on it. It will appear in the right-hand Monitor window. Push the play arrow to see the movie. Note the length of the clip in seconds. If you want to make it play longer than the time shown, go to step 7, otherwise go to step 8.

Step 7. Change the total time it will take to play the movie.

1. Make sure the clip is selected.

2. Be sure the timeline cursor is at the beginning of the clip, and the clip is at the beginning of the timeline.

3. Select File > Interpret Footage > Open.

4. The Frame Rate should be 30, if you are using an original clip.

5. Choose a new frame rate from the list below and type it into the text window. The new total time for the movie will be shown. Try different frame rates until you get the movie length you want. The following frame rates can be used: 1,2,3,5,6,10, 12,15,24,25,30

6. Click OK when you make your final decision

7. Click OK to the warning message that will appear.

8. If you now play the movie in the Monitor box, it will have the length you chose.

Step 8. Export the movie, file specification

1. Select File > Export > Movie

2. The Export Movie box will open.

3. Browse to the desired directory if different from the working directory.

4. Type in the desired file name, using the extension appropriate to the movie format (see below)

5. DO NOT CLICK ON SAVE YET!

Step 9. Make the movie format and codec selections

1. Click on Settings in the Export Movie box.

2. The Export Movie Settings box will open. There are five screens in this box. You can access them by the pull-down menu or by using the Prev and Next buttons:

General Settings:

File Type: Select Microsoft AVI or QuickTime

Range: Select Entire Project

Check Export Video

Check Open when Finished

Video Settings:

Compressor: (see "choice of codec", below)

Depth: (see "choice of codec", below.)

Frame Size: Normally use same as input images, but you can change it.

Do not check 4:3 Aspect. If you change frame size, be sure aspect ratio is unchanged.

Frame Rate:(see "choice of codec", below.)

Quality: (see "choice of codec", below)

Check Limit data rate to 1000 K/sec if an active choice

Audio Settings

(not used)

Keyframe and Rendering Options

Check Optimize stills

Field options: No Fields

Check Keyframe every and type in 1 frames.

Special Processing:

Click on Modify

The Special Processing box will open.

In the Special Processing box, check Deinterlace .

Normally, you should not make any other changes. However, you can crop your output movie if desired. You can also change the gamma (similar to brightness) if desired. The small image shows the result.

When finished with your settings, click on OK in the Special Processing box.

Step 10. Export the specified movie.

1. In the Export Movie Settings box, click OK .

2. In the Export Movie box, click Save

Choice of codec when using Adobe Premiere

For QuickTime

Compressor	Photo -JPEG
Depth	(not active)
Frame rate	same as you used in "Interpret Footage"
Quality	90%

For AVI

AVI movies with color images from surface-rendered models

Compressor	Microsoft Video 1
Depth	Thousands
Frame rate	30
Quality	100%

AVI movies with greyscale slice images

Compressor	Cinepak Codec by Radius
Depth	(not active)
Frame rate	30
Quality	90%

General Codec notes

• Quicktime with Photo-JPEG makes a smaller file than AVI with Microsoft Video 1.
• Quicktine with Sorenson did not give as good results as Photo - JPEG.
• AVI with Cinepak causes smearing of translucent portions of color images.
• The Cinepak codec is very slow in compressing the movie, but works well.
• AVI with Intel Indeo Video R3.2 works well, but won't accept large images.

Changing brightness or contrast of selected frames using Adobe Premiere

You must do the following before using "Interpret Footage"

1. Change timeline window options to show all the frames, if not already set that way.

2. Select the clip.

3. Expand the clip using the Zoom Tool until all the frames are visibile, return to the select tool.

4. Make a list of the frames that need to be changed, according to the time of each.

5. Right-click on the clip and select Filters.

6. Select Brightness & Contrast (add it to Current if it is not there).

7. Set the keyframe start and stop. The start should be one frame before the frame to be altered, and the stop 8. should be the frame you want to alter.

9. Select the first keyframe and set the brightness to the new value. NOTE: Alter the frame number BEFORE the frame you want to correct, EXCEPT FOR the LAST FRAME you want to alter. In that case, alter the LAST FRAME.

10. Select the second keyframe and set the brightness back to normal.

11. Export the movie: first with no compression to check; if OK, then use Cinepak compression. Cinepak compression may cause some "flashing" of individual frames if using "interpret footage" to increase the playing time. If this happens, try "clip>speed" for grey-scale images. This introduces some noise, but avoids the flashes.

Notes:

• If frames later in the timeline need to be altered, too, it is necessary to put TWO frame markers before later frames to be modified. The first of these should have the brightness set at the "normal" level. Otherwise, the brightness will gradually fade between the middle key frames.

• To make a movie which repeats a clip, "interpret footage" must be done first, before the clip is duplicated in the timeline.