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MCZ Collections Operations

Resources - Internal Protocols

Archiving Digital Media Protocol
(by mapping to MCZ shared drives)

The MCZ maintains a shared drive space for the storage of digital media of MCZ specimens. Collections can make use of this space to store media that meet archival standards outlined below and which eventually will be linked to MCZbase specimen records.

If a collection has difficulty following these outlined standards, this needs to be discussed before archiving can begin, so participation in future advancements can be insured. General oversight and management of the MCZ shared drive will be done by Brendan Haley, who will also coordinate departmental access.

Digital media of MCZ specimens produced by non-MCZ personnel should also conform to the protocol below, and should be obtained and archived whenever possible. A set of guidelines is available to help outside users in capturing media and metadata that fit MCZ standards and, more importantly, will save staff time and work. The distribution of this info and the archiving of the specimen media is managed by the respective collection.

File FormatS

Images should be captured in the camera's RAW format and converted to DNG, the preferred formats for raw images. Both the RAW and DNG files should be archived prior to any processing. For working with these file formats, the Adobe Camera Raw plug-in for Photoshop and DNG Converter are both freely available from adobe.com. The DNG file should be used for any necessary processing, and then converted to TIF, which is the required format for post-processing images. Click here for an illustration of this process. Collections Operations has developed a process and a Photoshop action sequence which automates the above workflow; please contact Collections Operations at the start of an imaging project to get this automated process implemented in your department. For images which are to be uploaded to MCZbase, please refer to the Workflow for Digital Media Projects policy page.

Naming Convention

In order to be consistent, clear, and informative, specimen images must be named according to the following convention: MCZ#, underscore, Genus, underscore, species, underscore, then (if applicable) letters to indicate the view of the specimen shown in the media, or a number to indicate that the media belongs to a series of images of the same specimen.

A list of standard abbreviations, which encompasses both animal and non-animal specimens, is provided to help departments with their naming conventions. As an example, the image of the dorsal view the head of a Boa constrictor would have the following filename:

      MCZ5460_Boa_constrictor_hd.tif

It is crucial to be consistent. Following the example given, all other images which show the dorsal view of a specimen's head should end with: “…_hd.tif”

Each department should keep a master legend of abbreviations used, including ones taken from the standard list provided. A copy of this departmental master legend should be given to Brendan Haley as it changes, and the standard MCZ abbreviations list will be updated accordingly.

In the paleontology departments, there will be specimen media that can't be easily categorized by "dorsal," "ventral," etc. To properly name these media, a two-digit number should be used after the species name to differentiate the media, and a special set of abbreviations should be used to clarify what's being shown in the digital media (please consult the "Paleo specimen" table in the list of abbreviations). For example:

      MCZ112334_Triarthrus_becki_01_counterpart_coated.tif

Organizing & Saving

Every department will have dedicated space on the MCZ shared drive for media which are linked to MCZbase. In each department's folder, there is a subfolder named "archival." This is where archival-quality media (which follow the format, filename, and organizing standards outlined above) should be transferred. When media are moved to the shared drive, they should be treated as read-only (i.e., never opened and re-saved), to maintain their archival integrity.

Raw digital mediashould be saved in subfolder archival\raw\[date] where [date] is the date on which the media were taken. Both RAW and DNG files should be placed in the dated folder.

Processed media must be saved in subfolders which are organized hierarchically. Higher-level taxonomic designations (class, order, family) provide good guidelines for folder naming and organizing.

In addition to placing digital mediaon the MCZ shared drive, each collection should take the responsibility to save media on a local hard drive and backed up on an external drive within their departments.

APPROPRIATE MATERIAL FOR ARCHIVING

Shared drive space should be used to archive images (or other digital representations) of MCZ specimens intended for hosting and display on the MCZ website, including MCZbase. All data deposited in the space must be in final, archival form as discussed above. For information about processing and uploading media for display on MCZbase, please refer to the Workflow for Digital Media Projects policy page.

Shared drive space is not intended to store data associated with ongoing research or educational projects by MCZ faculty-curators, postdocs, students and staff. Instead, these data should be stored on separate disk space established and maintained by the faculty-curators.

ARCHIVING video DATA

Video data of MCZ specimens should be stored on the shared drive in the appropriate department's media folder, in the "video" subfolder. Video data should be named in accordance with the guidelines above; use the abbreviation of the video resolution (480p, 720p, or 1080p). Archival data (the raw file(s) from the camera) should be stored in the "video\archival" subfolder, with each MCZ specimen's data contained in its own subfolder. This subfolder should be named as outlined above; for example:

     MCZ5460_Boa_constrictor_video

Deliverable files for MCZbase should be encoded as mpeg level 4 videos (MP4) sized at one of the standard video formats output by commonly available cameras (480p, 720p or 1080p), as well as 100-pixel-wide JPG thumbnails (screencap from the video); these should be stored in the "video\mp4" and "video\thumbnail" folders, respectively.

ARCHIVING audio DATA

Audio data of MCZ specimens should be stored on the shared drive in the appropriate department's media folder, in the "audio" subfolder. Audio data should be named in accordance with the guidelines above. Audio should be captured in uncompressed format whenever possible. The archival format is the least compressed original format of the file (for example, uncompressed WAV format, the preferred option on most digital recording devices). Archival files should be stored in the "audio\archival" subfolder, with each MCZ specimen's data contained in its own subfolder. This subfolder should be named as outlined above; for example:

     MCZ337250_Cardinalis_cardinalis_audio

Deliverable files for MCZbase should be exported from the original as MP3 and compressed at 192 kbps, unless the original was more compressed than this. This can be done easily with the free Audacity software. MP3 files should be stored in the "audio\mp3" folder.

ARCHIVING MICRO-CT DATA

Micro-CT data of MCZ specimens should be stored on the shared drive in the appropriate department's media folder, in the "ct data" subfolder. Micro-CT data should be named in accordance with the guidelines above; use the abbreviation "3d" for 3d reconstructions (WRL format files). Archival data (the original data generated by the Micro-CT scanner and system) should be stored in the "ct_data\archival" subfolder, with each MCZ specimen's data contained in its own subfolder. This subfolder should be named as outlined above; for example:

     MCZ5460_Boa_constrictor_3d

Deliverable files for MCZbase are WRL files and 100-pixel-wide JPG thumbnails; these should be stored in the "ct_data\wrl" and "ct_data\thumbnail" folders, respectively.


For more information on any of these issues, please contact Linda S. Ford at Collections Operations.