Photo management

First off, go play with this interactive map of our sampling locations on our project homepage, because I’ve been working on it for the last week and I’m very proud of it :).

Now, I have a confession to make.

Despite the singular focus of my prior blog posts, my work is not entirely composed of swimming around in the tropics. In fact, most months of the year, you can find me right here, bathing instead in the light of my computer screen.

I’ve been meaning to write more posts while stateside, but the subject matter is a bit more difficult to ‘spice up’. So I’ve put it off. Today, however, I think I’ve got an interesting topic that will begin a new theme of post regarding the most interesting and time-consuming part of my job: computer work.

Since we returned from Reunion a couple of weeks ago, I’ve spent a considerable amount of time preparing the photos and data from our trips so that they are organized, useful, and publicly accessible. So far, the team has collected over 3,000 photos of more than 550 coral samples. Keeping these organized can become very difficult as we progress, so I’ve been working with a variety of tools to make it easier. When we’re in the field, we take tons of photos of each individual coral, from closeups that show small morphological details, to wide-angle photos that we can use later to determine the surroundings of the coral. We also take photos of the reef, photos of each other, and photos of that awesome creature that I’ve never seen before and it’s so close and so colorful and sooo cool and look at it feeding, it’s waving its antennae around and catching things and it’s so awesome!!

Seriously, this mantis shrimp was freaking cool

Seriously, this mantis shrimp was freaking cool

At the end of the day, I have hundreds of photos. Some are pretty, some need post-processing work to become pretty, some are definitely not pretty but can be used as data, and some might be useable as data with some post-processing of their own. Each photo might have one or multiple samples in it, or could be a great example of a particular disease, or maybe just it just has one of us making a funny face. To be useful, I need a way to find these photos again, somewhere in the midst of the 47,000 other photos on my hard drive (seriously).

Ummm... data?

Ummm… data?

The primary tool I use to manage the mess is Adobe Lightroom. Lightroom enables me to process my photos in bulk and add keywords to the photos so I can easily search for them later. When I import all the photos from a particular dive, for instance, I have Lightroom automatically add the GPS coordinates for the dive and keywords for the site name, project, photographer, etc. Then I go through the photos and add keywords to each one that include sample identification codes and everything interesting in the picture, like fish, diseases, or divers. Now, there are two very neat aspects about Lightroom keywords that I take advantage of. The first is that you can establish keyword synonyms so that every time you tag a photo with one word, its synonyms will automatically also be attached. I can tag a photo with ‘lionfish’, and that’s all well and good. But later, I might be thinking all sciency and want to find all my photos with ‘Pterois radiata‘ in them. If I have previously told Lightroom that the scientific name and common name are synonyms, my search will find exactly what I need.

But what if I want to find all photos of fish that belong to Scorpaeniformes (the group that includes both lionfish and stonefish)? The second handy aspect of Lightroom keywords comes in here: they can be placed in a hierarchy. I’ve placed the keyword ‘Pterois radiata‘ within ‘Pterois‘, within ‘Scorpaeniformes’, so every time I tag a photo with the simple term ‘lionfish’, it’s also tagged with its higher-level taxonomic groupings. For our samples, I even put the sample ID keyword within its corresponding species. In fact, I’ve set up an entire taxonomic tree of organism names within my keywords, so every time I tag a simple sample ID, the photo is made searchable with terms corresponding to all the different levels of the tree of life. It’s awwwesommmmeee.

Manual keywords (5): E10.17.Cyp.sera.1.20150628, North Bay, Octopus, Photo by Joe Pollock, GCMP Sample
Resulting keywords (29): Animal, Anthozoan, Australia, Cephalopoda, Cnidaria, Cnidarian, Cyphastrea, Cyphastrea serailia, E10.17.Cyp.sera.1.20150628, GCMP, GCMP Sample, Hard coral, Hexacorallian, Indo-Pacific, LH_282, Lord Howe Island, Merulinidae, Metazoan, Mollusc, North Bay, Octopus, Pacific Ocean, Photo by Joe Pollock, Protostome, Robust, Scleractinian, Stony Coral, XVII, AU

The next stage of photo management for me is post-processing. I am nowhere close to an expert photographer or image editor, but I’m learning. It’s still amazing to me how much a photo can be improved with a couple quick adjustments of exposure and levels. Most of the time, photos seem to come ‘off the camera’ with a washed-out and low-contrast look. Underwater photos always have their colors messed up. When we take photos of samples, we generally put a standard color card and CoralWatch Coral Health Chart in the frame so that we can make the right adjustments later. Fixing the color and exposure doesn’t just make the photos prettier, it can help us to understand the corals. It’s tough to spot patches of disease or the presence of bleaching when the whole photo is various dark shades of green. The best thing about Lightroom (at least compared to Photoshop and a number of other image editing programs)* is the ability to make adjustments in bulk. Often, a particular series of photos were all taken in very similar conditions. Say, all the photos from a single dive, where we were at 30 ft with a particular amount of visibility and cloud cover. I can play around with just one of the photos, getting the adjustments just right, then simply copy those adjustments and paste them to the rest of the photos from the dive. Voila! Hundreds of photos edited.

Before adjustments

After adjustments

Aaaand before

Aaaand before

Aaaannd after

Aaaannd after

Once I’ve got the photos edited and organized, I can do fun things with them, like export them to Flickr for your browsing pleasure, or embed them in the map you explored at the beginning of the post. But explaining that is for another day…

*A note about software. The next-best photo software I’ve used is Google’s free (free!) Picasa. Picasa will also allow you to batch-edit photos, and had facial recognition long before Lightroom. iPhoto also has these features. But as far as I know, the keywording in Picasa and iPhoto doesn’t support hierarchies or synonyms.

Merci Beaucoup!

Although we generally like to post all the fun details of our project, doing fieldwork internationally is hard. Mountains of paperwork and preparation go into our trips (much of it often stressful and last-minute), and when we arrive, we generally don’t know the local corals very well, don’t know the language as well as we think we do, and don’t know the area at all. We’re learning as we go about all the best ways to make our trips go smoothly.

But for now, as I sit in the Paris airport on my way home, I’d like to give a shout-out to all the people who have helped make this particular trip happen. One of the first contacts Jerome made on the island was with Le Club de Plongee Suwan Macha – an organization of SCUBA divers that works like a co-op, buying and maintaining resources that are shared by members at a very affordable price. This system worked great for us as a way to get many customized dives in and seems like an awesome set-up for scientific diving in general. We even borrowed a few tanks of air for some of our ‘labwork’, unrelated to diving. After we joined the club, the acting president, Pierre Grisoni, volunteered his time to drive the boat and refill tanks for us for all the dives we did on the West coast of the island. These dives were essential to our collections and formed the core of our trip! Merci beaucoup à Pierre and the rest of the club!

Thanks, Pierre!

Thanks, Pierre and Suwan Macha!

Another important contact was Dr. Jean-Pascal Quod, president of Reef Check France and manager of Pareto Ecoconsult. Jean-Pascal and the diving club SUBEST were instrumental in our collections on the East side of the island, and showed us some really great reefs over there.

Perhaps the most important local entity was The Natural Marine Reserve of La Réunion (RNMR), which provided us with local collections permits and prepared our CITES export permits. Dealing with this paperwork is often the most difficult part of our work, and being able to work with the local management authority is essential to our project.

Many other people have been helpful on this particular trip. For starters, I bummed a ride to and from the Portland airport with my parents, which is excellent. I also left my car with them and got lots of other help from them before leaving. I believe Amelia’s mother also took her and Jerome to the airport, after quickly sewing together my BCD weight pocket for me. Ummm, awesome!! Then there’s Jerome’s mom, who on multiple occasions hosted us all for outstanding dinners while we were in Reunion. Everything’s easier in life with parents like these!

Les parents

Les parents McMinds: merci for all you do

We also met many of Jerome’s friends and family while there, and a number of them provided us with delicious food, too. Thank you to all of you for showing us your island and making the trip great!

Since we first started planning the trip, there has been one person who made the right contacts, spoke the right language, and put in a lot of effort to get all the permitting and paperwork done on the French end of things: our postdoc Dr. Jerome Payet. In addition to pre-trip organization, he also acted as our guide, facilitator, translator, and co-director throughout the trip. I’ve worked with Jerome a lot in the last couple years, and he has been an integral part of the lab for a bit longer than me, but working on this particular project was generous of him. This trip came at a special time for Jerome, as well, since he is now moving on to work with a different lab at OSU. The work he put into it is thus very much appreciated. Thank you – we will miss you!!

Au revoir, Jerome

Au revoir, Jerome