Table of Contents
Media should be a key component of any MorphoBank project. Virtually all MorphoBank projects include media, and many contain hundreds or thousands of media items. (Because MorphoBank supports video and audio files as well as imagery, the more general term "media" is used in place of "images.") MorphoBank allows you to upload as many media as needed, to use media to document scorings in your matrices and to assemble media into annotated groupings ("folios" - see Chapter 13, Folios) for online publication.
Regions of uploaded images may be labeled using tools integrated into MorphoBanks's high-resolution pan-and-zoom image viewer. If the labels are added to an image in a matrix cell the labels will be associated specifically with that cell and automatically include the taxon and character names.
Uploaded media can (and should) be tagged with the specimens they depict as well as a view descriptor (see the section called “Media views”). relevant citations from your project bibliography and Darwin Core-compatible metadata. A media browser allows project members to conveniently browse and filter large quantities of multimedia data.
Original uploaded media files are always retained by MorphoBank and may be downloaded at any time. Thus, you should always upload your media at a resolution and quality suitable for research work, even if that file is too large for convenient use on the web.
MorphoBank will automatically convert uploaded media to web-viewable formats at appropriate resolutions and quality for web use. This largely frees you and your collaborators from tedious media conversion tasks. If your files are in any of a number of mainstream formats no pre-processing on your part should be necessary.
MorphoBank includes a built-in image viewer that allows users to pan-and-zoom over a full-resolution version of your images. Because it sends only the portion of the image that is actually visible, even very high-resolution imagery is usable on a normal internet connection in MorphoBank. The image viewer also supports image labeling functions.
MorphoBank accepts a variety of image formats including JPEG, GIF, PNG, TIFF and Photoshop. Note that Photoshop files that use layer effects may not render properly on MorphoBank. For the most consistent results we recommend converting these files to TIFF format before uploading. All image files should be in RGB mode. Files in CMYK mode will probably not render properly. You should upload image files at the highest resolution that makes sense for your project. MorphoBank will automatically create sized versions for use on the site as well as a full resolution version optimized for online viewing. The original uploaded file is retained and made available for download. MorphoBank also accepts the following audio/video file formats: RealMedia, QuickTime and WindowsMedia. MorphoBank does not support the PowerPoint file format. If you need to use images from a PowerPoint presentation, you should export them from PowerPoint in a supported format such as JPEG and then upload those files.
The preferred video file format for upload to MorphoBank is MPEG-4 (with or without h.264 compression). Files in QuickTime and WindowsMedia format will usually work so long as the compression method used is supported by MorphoBank's video processor. In general, videos compressed with versions of WindowsMedia prior to version 10 will work, as will most QuickTime compression methods (some very old and rarely used methods like GIF compression are the notable exceptions). AVI files usually will not work and should be converted to MPEG-4 prior to upload. MPEG-2 (.MPG) files also will not upload. In general if your uploaded file is being rejected by MorphoBank it is recommended that you try re-encoding the file in the MPEG-4 format using one of the many video conversion tools available for Mac OS X, Windows and Linux.
Audio files may be uploaded to MorphoBank is MP3, AIFF or WAV format.
Other formats, such as AAC, are not supported. If you need to convert or
edit your audio files use a sound editing application such as Audacity
To add a media file to your project, click on the
media button in the button bar. You will be presented with
a form like the one below.
Use the "Choose media file to upload" file browse button to pick a file to upload. It must, of course, be in a supported format or it will be rejected. To pick the specimen from the project specimen directory that this media item represents, type the first few letters of the taxonomic name catalogue number or institution code into the "Specimen" text entry box. A menu will appear with all possible matches, as shown below. The more you type the more specific the list of possible matches will become.
You can tag your image with one of the views, as configured in the
Views tab by choosing it from the "View"
drop-down menu. Choose "- NONE -" if no view is applicable.
If the image is under copyright, be sure to check the "Is under copyright?" box and enter the copyright information (year, holder, contact information) into the "Copyright holder" text entry field.
You may add notes to the image using the "Notes" field. Notes are private to the project and are not published. If your image was obtained on the Internet you can note the URL from which it was obtained and any documentary information in the "Url of media" and "Url description" fields.
You may optionally attach a bibliographic reference to the image by typing in the first few characters of the reference title or author name(s) into the "Find bibliographic reference" box. You will be presented with a list of possible matches from your project bibliography from which you can choose the appropriate reference.
The only data absolutely required is the media file itself. You are strongly encouraged to specify a specimen from the specimen directory for each media item. The matrix editor uses the specimen taxonomy to suggest relevant media for placement in cells. Thus media without specimen data will not be usable in matrices.
You should also specify copyright information for your media, if applicable. The earlier this is done the fewer copyright clearance problems you will encounter later as you move towards publication.
File Space is a holding area for media that
are not yet part of a project. You can upload media in batches to the file
space and then add individual files in rapid succession to a project from
the file space, rather than uploading files one by one. This can be a major
time saver for projects with large pre-existing collections of media.
Each MorphoBank user has her own File Space, the contents of which is not shared. Files in your File Space are not visible to anyone but you until they are added to a project.
To upload a batch of media (images, video, sound, etc.), you must convert the batch of files to a single archive file. The file space will accept archives in either Zip or Tar format. Tar archives may be optionally compressed with Gzip or BZip2. To create Zip archives on Windows, you must use a program like WinZip. On Mac OS X, simply control-click on the folder containing the images and select "Create archive" from the pop-up menu.
Your archives can contain files in any supported format. Unsupported formats will be ignored. You may group files in nested folders. The folder structure you create will be preserved in the file space. You may also upload individual files in the listed formats. Please note, however, that when uploading a single TIFF or PSD format file it will often be faster to upload a compressed archive containing the file than the file itself, unless it is a TIFF saved with LZW compression. Compressing single files in the other formats is generally not worthwhile.
Your archive must be no greater than 32MB in size. Archives exceeding this size will be ignored.
In the top-level tab bar of the MorphoBank navigation bar is the
File Space tab. Clicking on it will display
the contents of your file space and two tabs:
Contents (which will be selected) and
Clicking on the
Add Files tab will display
some text explaining how to use the File Space and a "Choose a ZIP, TAR,
TAR+gzip, TAR+bzip archive or individual file" file browse button. Click
on the button, choose an indivudual media file or an archive with many
files, then click on the "Upload archive to file space" button.
Uploading large archives can take a while. Once your archive has
uploaded and been processed, MorphoBank will return an inventory of
files that have been successfully added to the File Space as well as a
list of those that were rejected. Accepted files are visible in the
Contents tab immediately after acceptance.
To add media from your File Space to a project, simply open the File
Space and click on the media. You will then be presented with a form
like the one shown in Figure 10.1, “New media upload form”,
except that the media file is pre-filled. Simply fill out the form as
you would for media added with the
button and click "save."
Note that the File Spaces are private to users, not projects. This means that not only is your File Space the same across all projects you are working on, but it is not shared with other project members. It is private to you.
|Since the file space is the same for all projects you are working on, make sure you are in the correct project before adding media.|
You can upload batches of media
directly into your project using the
upload tool. This is in contrast to the
space which allows you to upload batches of media to a
holding pen for subsequent addition to a project on a 1-by-1 basis along
with metadata such as specimen, notes and copyright information. The batch
tool will add any number of media directly to your project in a single step
and is thus much more efficient than the
space. However, all of the media in the batch will have the
same metadata. Which tool you use depends upon the nature of your media (and
project). If you have quantities of media having the same copyright,
specimen or descriptive text then the
tool is probably the right choice. If you have quantities of media with
widely variable metadata then the
file space is
likely a better choice.
To use the
batch upload tool, click on
add media batch button bar. You will see a
screen like the one shown in Figure 10.3, “The media batch upload tool”. Under the
header "Choose a ZIP, TAR, TAR+gzip, TAR+bzip archive or individual file"
click on the file browser button and select a batch of media compressed as a
ZIP, TAR, TAR+gzip (.tgz) or TAR+bzip (.tar.bz2) file. Fill in any of the
other fields for which you have data. To select a specimen type the first
few letters of the specimens name into the text entry. A list will appear
with possible matches. Similarly, if you wish to link a bibliographic
citation to the uploaded media type the first few letters of the references'
title or author and then pick the relevant reference from the list of
possible matches that appears.
When you are done click on the "upload archive" button. When the upload and processing is complete you will be presented with a summary of results from batch processing.