A Picture’s Worth 1000 Data Points: Tips for incorporating photos into our science

Scientists take a lot of pictures, or at least, we should. We travel to unusual places, do unusual activities, and see unusual things, all of which can often be displayed excellently in a photograph. Before cameras, many scientists were also supreme artists. They would document the real world (and the subjects of their studies) in drawings or paintings, and the line between scientific data and artistic expression was blurry. This skill was necessary for the dispersal of information, and more information on a place or a organism can often be expressed per page in a picture than in text. A collection of dozens of paintings or drawings could represent a lifetime’s work and only exist in a handful of prints. Now, with digital photography, we can take hundreds of high-quality photos in minutes with infinite, diverse data and immediately share them with the world. But all these photos can be difficult to manage, particularly as your collection grows. So let’s talk about how we can more effectively manage our photographic

Most science-pics can fit into at least one of four categories: 1) Aesthetic, 2) Exhibitory, 3) Methodological, and 4) Systematic. Aesthetic photos should be consciously composed and executed, and serve as an artistic representation of a subject. Handy for presentations and exhibits, these can be infinitely elevated and the principles that make a quality photograph can be incorporated into any picture, scientific or not. Exhibitory photos are particularly useful to scientists seeking to communicate natural phenomenon. If we carry a camera with us while we’re in the field, we can catch examples of our study topic in action. For example, a photo of a bird eating a bug on a cactus can help you explain the idea of indirect facilitation. Again, these types of photos are useful for presentations, teaching, and publication, but do not necessarily have to be artfully composed (though an attractive photo can make your presentation stronger and more professional). Methodological photos are unique, but are present across many disciplines, as a tool or resource for explaining a protocol. For us ecologists, these photos are usually of a researcher conducting their experiment or of equipment in the field. A photo like this can help your audience better understand what exactly you were doing, especially if they are outside of your field. And finally, systematic photos are those which are taken as a part of the protocol. Just like any other measurement in a study, these photos should be taken at regular intervals, be they spatial, temporal, or event-based. These photos are often not aestetic at all, but rather are primarily functional. One should never permanently delete these photos just are you wouldn’t delete other observations–they are a part of the dataset. Indeed, this category is usually the type of photo that requries the most management, and is most likely to make your hair fall out. Large file sizes make it hard to save on your personal machine or online platform not specifically designed for uploading many photos at once (looking at you, google drive). That’s why I’m going to tell you a bit about a platform that we can use to more effectively backup, share, and manage our science-pics: Flickr.

Flickr, an online photo sharing platform, is similar to many other databases were one can have their own personal account, be on a team account, create groups, tag photos, and make your photos public or private. Free for your first 1000 photos and $50/year for unlimited uploads, the real beauty comes in it’s file management. And lucky for us, it has both a desktop and mobile version. Just like any platform, however, it has it’s disadvantages. Without careful monitoring and guidelines, it can become just as unorganized and hence unusable as any sharing platform. To benefit from Flickr’s system, you have to establish a system among your team, and make sure to follow it. Here, I’m going to walk you through uploading a photo, creating an album, and managing those photos in a clean and effective way.

Once you’ve signed in you, you can explore your profile page, which has different tabs for the different elements of your page. This is pretty self explanatory; the only part that may seem confusing is the Photostream element, which is simply a list of all public photos you’ve uploaded in order of recentness. Private photos won’t show up here.

The Ecoblender Lab Profile page. Notice the Photostream is empty because we are new account.

Our profile page won’t be very interesting, however, until we start to populate our account by uploading photos. To do this, notice the cloud and arrow in the top right corner and choose “Upload”.

To add any new photos, you’ll need to upload. You can pick the different settings and details (like what album you’re adding to) during the uploading process.

Now, to upload new photos, simply follow the prompts and fill out the left hand tabs with descriptions or tags, and chose/create the appropriate the album. You don’t need to choose an album, if you don’t, it’ll simply go to your camera roll and (if public) your photostream. However, we should always try to maintain order by depositing photos into albums, especially on a shared account.

More tags means more potential viewers! That is, if it’s public.

But the real power comes when we want to upload multiple photos at once. Unlike other photo sharing platforms and most personal machine file management systems, you can edit multiple files and assign names/descriptions/tags/people/albums to multiple files at once, easily selecting all or some of the photos you’re interested in.

Edit the details for all, one, or some of the photos you’re uploading.

Now, if you are working on a project that includes systematically taken photos, a team Flickr account can support it. It’s important to establish certain guidelines for the publication for all albums with multiple contributors, but especially for photos a part of a dataset. As an example, our lab is cataloging photos of trees on York University’s campus, and we would like to include photos of every tree in an album on Flickr. We might use the following guidelines to make sure all photos are properly documented:

  • Album title should be descriptive of the project and include the year.
  • Only systematic photos should be included in the album, methodological and fun photos should be in a separate album.
  • The photo title should be the Unique ID that the tree is recorded as in the dataset. If we have multiple photos for one tree, that’s fine! Maintain the
  • The description should include any details that distinguish it from other photos of the same tree (e.g. you might take a photo of the entire tree, a photo of a bird in the tree, and some damage to the bark, so include that detail in the description). Try to use the same one or two words if you are taking the same photos (e.g. “whole tree”, “bird”, “damage”, etc.). It should also include the photographer, the date the photo was taken, and the treatment we are interested in (for this project, it might be disturbance level).
  • We should include general tags on every photo that strangers may wish to find (e.g., science, ecology, nature, explorer, tree, bird, insect, etc.), but also a project-specific tag that includes systematic and other photos from the project.
  • The members working on the project should be added to “people”, particularly those who were collecting the data (even if they weren’t the photographer)

This is only one example, but it can be modified for all sorts of albums and projects. In fact, it doesn’t have to only be for specific projects! How often have you been working on a presentation and realized you never did take a photo of your study site? Instead of trying to track down anyone with a photo of the place (or being asked to wade through your phone’s camera roll), we can have a place to put them all immediately and know exactly who to credit (don’t forget to credit photographers!) When we systematically organize our photos, we can quickly find and share them among our peers. Much like sharing our code, our research plan, or our datasets, sharing our photos can help cultivate a culture of open science and provide resources within our own research group and beyond! Now, go follow us on Flickr, @ecoblender_lab! 🙂

SC/BIOL 4000 8.0 BIOLOGY HONOURS THESIS

This Fall will be remote for the majority of academic activities. The 8.0 credit honours thesis program is approximately 8mos in duration. The student leads an independent research project. As a team, we would like to work with two individuals on one of the following projects. Each student will work with a graduate student or postdoc and Chris Lortie.

a. Each project is individually implemented by the student safely.
b. Zoom calls with Chris and the co-mentor to ideate, solve, and plan will be used to collaborate in addition to editing datasheets and docs.
c. It will be beneficial for the student to have experience in R and be able to work independently.
d. The pre-reqs are listed online for BIOL4000 are here and currently include students their final year with a BIOL GPA of at least 6.0.

Tree forest dynamics at YorkU

(1) Subway effects on trees and woodlots. A census of tree forest dynamics and individual tree changes on YorkU campus. Jenna Braun, Mike Belanger, and I dug through census records compiled by the YorkU master gardener in 2012 and 2013. Over 5000 trees were tagged on campus and their size and health were recorded. The data are here. This is a fantastic project and opportunity to revisit a superb dataset in R and also resample some or many of the trees. We now have a subway rumbling away underneath campus, and we can check trees near and far from the line and test the hypothesis that disturbance belowground influences tree growth and health.

(2) Other ecological hypotheses relevant to urban forest dynamics (disturbance, new buildings, edge or center of campus etc). There are at least two projects here. The students can work independently and still split up the work of testing more than question or hypothesis. One individual can (re)sample trees from 2012 and 2013 near/far subway lines, and a second student can examine any other ecological question with disturbance, new buildings, or how sets of trees are doing in different ecological contexts on a university campus.

Desert ecology data analyses

We have many open datasets ready to go for deep analysis work if you are competent in R (or Python but we work in R in the lab). Many spatial questions, niche questions, or use or plant and animal survey data and join them to new data on climate or downscaled remote data if you are game for that adventure. Here are a few examples.

Vegetation under shrubs and in the open in the Central California Deserts.
Data.

Desert arthropod diversity patterns in California.
Data.

Camera traps and birds of the deserts.
Data.

In each instance, the workflow will include a few Zooms to plan analyses and additional data lookups, then the student researcher digs in!

To apply

If you meet the pre-reqs and are in your final year in YorkU Biology, please email lortieatyorkudotca, and we will set up an interview with you for the team!