All posts by Peter Staub

Botanising with ColectoR: a field report

A few weeks ago, I went hiking on Mt. Pilatus with a group of plant enthusiasts. I decided to use our excursion to test ColectoR, a new smartphone app, which the developer claims to be a „digital field notebook for voucher specimen collection“. You can find the results of this test in this first post of our blog, which will hopefully see more updates in the near future.

Lucerne’s early 14th-century Kapellbrücke with Mt. Pilatus in the background.

Background

Smartphones have entered almost every aspect of our lives. As mobile service terminals they provide tools such as for dating, stargazing, micropayments and even for fighting food waste. Smartphones are versatile because they provide a powerful combination of features, such as GPS, camera and mobile internet connection.

As a digital native I was interested to see the recent surge of online species observation apps that make use of smartphone sensors, such as the popular iNaturalist and PlantNet. Today, there exists a range of such tools, all of which have different geographical (global/local) and taxonomic (plants/animals/fungi/etc.) scopes, and different target audiences (lay/professional).

Unfortunately, the more well-known apps/platforms available in the Android app store were not to my satisfaction as they tend to be overloaded with features and cumbersome to use. Why do I have to register my email-address before using the app? Why would I need an unknown specialist to review my plant identifications? Why do I have to automatically upload my plant collection data to a remote server? Despite the sheer number of platforms, I was puzzled over the lack of a simple app that just replaces my field notebook, no matter where I am, no matter if there’s a mobile data connection, and without the usual bloat of functions. Moreover, as I regularly botanise outside of Switzerland, I was looking for an alternative to the online field book FlorApp by Infoflora, which, apart from its geographical limitation to Switzerland, is very useful.

Introducing ColectoR

I discovered ColectoR about two months ago when preparing some slides for a talk. Actually, I stumbled over it by accident while browsing the web for applications of smartphones in biodiversity research. ColectoR seemed to be the perfect example of an app that makes use of smartphone sensors and capabilities and combining these in a powerful manner. According to the developer the app was created “to aid botanists in the collection of data for voucher specimens using smartphones”.

Overview

ColectoR’s user interface consists of five separate windows:

  1. A start screen
  2. A page to enter plant collection data (plus icon)
  3. A window to manage all entries (eye icon)
  4. A data export window (cloud icon)
  5. A settings pane
a) This is the start screen. By pressing the + you can create a new record. b) Page to enter plant collection data. C) Overview of all collected vouchers.

Entering data

By pressing the plus icon on the start screen you reach the data entry window. On this page, there are separate fields for entering the data that are usually jotted down in a field notebook. Just fill in the date of collection (automatic or manually), the collector (stays the same by default), collection number (auto-incremented), species, author, family, description, latitude, longitude and altitude (all three of which are drawn from the GPS receiver, if turned on). Further, data for country, state and locality are automatically drawn from Google Maps, again, if the GPS is on.

Page to enter details on voucher specimens; a) Name and collection number are filled in automatically; b) Species names can be checked using an online name-resolver database; c) the corrected species name is filled in along with the botanical family.

Apart from this basic functionality, there are two additional fields for taking notes. The cool thing about these fields is that data can be entered not only manually but also through voice recognition (if you’re not scared of sharing your data with Google). Voice recognition is done by pressing the microphone icon, which accesses the Android native voice recognition system. Quick tests in both German and English worked almost perfectly (no more tedious scribbling in the field notebook!).

Notes can be taken manually or via voice-to-text. a) Androids native voice recognition at work; b) text is automatically entered.

Another nice feature is the spell-/synonymy-check function for species names, which also returns the correct family name (magnifier icon, mobile data connection needed). For this, ColectoR connects to the iPlant Taxonomic Name Resolution Service. In many cases, this name check worked fine, even with minor typos in the query. In cases with two or more typos in the name, the algorithm often did not return any result, but that’s ok.

There was, however, one little drawback with this feature. Specifically, the name-resolver returned an unaccepted synonym, when I name-checked Persicaria bistorta (L.) Samp., which is an abundant species growing on montane and subalpine meadows. While I myself know this species under its (synonymous) name Polygonum bistorta, the name-checker suggested Bistorta officinalis Delarbre as the correct name, which is yet another synonym of the currently accepted name Persicaria bistorta (L.) Samp. (The Plant List). This means that the auto-check function did not return the currently accepted name, but just another synonym. It thus seems that this service is not fully up-to-date. Of course, returning the wrong synonym is often not that big of a problem at all as the synonyms are equivalent to the accepted name. However in cases where the taxonomy o a species is not well established, this may cause trouble.

Persicaria bistorta (L.) Samp.

Yet another cool function is the option to take pictures and link them to specific vouchers (camera icon). Having the option to take more than one photo per record greatly facilitates the documentation of features that are difficult to fit into one photo (such as umbels and pinnatifid leaves of Apiaceae species.

Taking diagnostic pictures of plant features with smartphone cameras can be difficult. This is why the option to take more than one photo per record helps.

Data management

If you wish to review your records, you can access the entry management window by hitting the eye symbol on the start screen. This will give you an overview of all vouchers collected so far. From here you can easily edit or delete your records. Accidental modification is prevented by the lock icon in the upper left corner (the current record is grayed out). Entries can be edited only after unlocking.

By default, all records are protected (greyed out). Unlocking can be done by pushing the lock icon in the upper left corner.

Data export

After the trip, the collected data can be exported with two different functions. Voucher data can be exported as a tabular form (*.csv). Photographs can be saved in the form of an archive (*.zip) with the pictures put into separate folders according to the respective collection number. Multiple pictures per voucher are possible. Both photos and collection data can be exported through the usual android share menu, meaning that you can choose, for example, to mail the data, to share them via cloud storage or to store everything on your phone.

The implementation of such an open data export interface has many advantages, most importantly, that downstream data analysis can easily be integrated into your workflow. For instance, the data can be automatically transformed into labels for herbarium vouchers. The developer actually offers a ready-made solution for this on his website. Another possibility for downstream data processing would be to automatically plot a map of all collected vouchers based on the coordinate data.

Two of ColectoR’s five basic windows. a) Data export page; b) settings pane (the default values worked fine with me).

Performance

I haven’t done extensive performance testing, so I can’t say much about this. Battery life was not an issue on our hike, but surely might be one on longer trips. Probably it helped that I turned on the GPS only when needed. Of course, the usual battery-saving tips apply: reduce screen brightness, turn off Bluetooth and WiFi, change your screen to grayscale, etc.

Future

According to the developer, ColectoR was initially created in 2014, and since has received multiple updates. It can only be downloaded from the developer’s website and not from the usual app stores. Currently, the app is only available for Android. However iOS and Windows Phone versions are planned.

Conclusion

In conclusion, ColectoR is of potential interest to all plant-lovers with at least some background in botany. People without knowledge of plant species will miss some form of assistance with plant identifications. The app represents a smart combination of features that simplifies a botanist’s life on field trips. The app convinces with its tidy graphical interface, different possibilities for automating your workflow (without being patronizing) and it’s open license that allows for further software development. In short, ColectoR fills a niche in the app ecosystem that has been open for too long.

Pros (there are many)

  • Free and intuitive to use
  • Can be controlled with just one hand
  • Supports voice-to-text
  • Straightforward data export
  • Easy integration with downstream data processing (e.g. R)
  • Low battery-consumption (when GPS is turned on sparingly)

Cons

  • Height data sometimes not very accurate in the test
  • Name resolver sometimes does not return currently accepted name
  • Smartphone camera of limited use for plant photography

Research in Ethnobiology: a new blog

Ethnobiological research covers a wide range of topics, from fundamental botanical field surveys to livelihood analyses and market research to highly specialised statistical methods.

The aim of this blog is to present and discuss some of these methods. This is work in progress, and we encourage everyone with skills and knowledge to contribute to this collection. Please contact Franz Huber, at huber@ethnobot.ch