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Data management and processing tools / Feed

Conservation tech work doesn't stop after data is collected in the field. Equally as important to success is navigating data management and processing tools. For the many community members who deal with enormous datasets, this group will be an invaluable resource to trade advice, discuss workflows and tools, and share what works for you.

discussion

Automatic extraction of temperature/moon phase from camera trap video

Lucy Dimitrova

29 November 2023 1:15pm

Hey everyone, I'm currently trying to automate the annotation process for some camera trap videos by extracting metadata from the files (mp4 format). I've been tasked to try...

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John Loehr

7 September 2024 9:44am

I just noticed that TrapTagger has integrated AI reading of timestamps for videos. I haven't had a chance to try it out yet, but it sounds promising. 

John Loehr

28 October 2024 7:30pm

Small update. I uploaded >1000 videos from a spypoint flex camera and TrapTagger worked really well. Another program that I'm currently interested in is Timelapse which uses the file creation date/time. I haven't yet tried it, but it looks promising as well. 

Michal Smielak

1 November 2024 12:29pm

Hi Lucy,



I now realised it is an old thread and you most likely have already found a solution long ago but this might be of interest to others.

As mentioned previously, it is definitely much better to take moon phase from the date and location. While moon phase in general is not a good proxy for illumination, that moon phase symbol on the video is even worse as it generalises the moon cycle into a few discreet categories. For calculating moon phase you can use suncalc package in R but if you want a deeper look and more detailed proxy for moonlight intensity, I wrote a paper on it 

 with accompanying R package called moonlit 

When it comes to temperature I also agree that what is recorded in the camera is often very inconsistent so unless you have multiple cameras to average your measurements you are probably better off using something like NCEP/NCAR Reanalysis (again, there is an R package for that) but if you insist on extracting temperature from the picture, I tried it using tesseract and wrote a description here: 

 

Good luck!

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discussion

How do you fund or finance your long-term data infrastructure?

Frank van der Most

12 September 2024 5:28pm

Today at the Bioacoustics Data Networks and Platforms webinar during the after hour, there was a great discussion about long term data infrastructure. Not just how to...

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Frank van der Most

24 September 2024 2:35pm

Hej @kimhendrikse,

Not really the kind of answer I was looking for ( because we now still don't know how you finance your setup ), but it is an interesting answer to the question which is also practiced here and there. But the financing problem will not disappear. It will just be distributed as well. The nodes still need funding. Less so per node, which might make it a lot easier, but there is still funding involved. Perhaps there is even a way to distribute the 'central' catalogue. I wouldn't insert a central repositoring chaching data because then we're back at something big and expensive again. 

Also, there will be costs involved in developing and maintaining standards, which also need to be paid - through membership fees perhaps. Lastly one would need a way to deal with those nodes that cannot fund themselves anymore. It would lead to fewer and bigger nodes and should not happen too much because then we're back at square one.

 

Kim Hendrikse

24 September 2024 2:44pm

"because we now still don't know how you finance your setup"

I pay for everything myself out of the salary from my full time job :-(

But... long term I'm seeing a future in starting a company that sells products. (Maybe not that long term).

Frank van der Most

24 September 2024 3:42pm

That's a really honest answer Kim! Thank you for clarifying

You're likely not the only one. In fact it would be interesting to find out how much conservation tech use and development is funded through personal means. I made a note. Perhaps we'll do a poll sometime

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event

Design-led innovation for nature

Catherine Greene

20 September 2024 2:24pm

How can space-enabled data and services be translated into information that is trusted and actionable, fuelling responsible behaviours towards nature? A new programme where SMEs will be paired with design consultancies...

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discussion

efficient methods for labeling clusters of fish in images for segmentation purposes 

Tongfei Yang

16 July 2024 9:43pm

Hi everyone,Our team is working on a project involving the segmentation of individual fish within clusters (groupers specifically). We have images with hundreds of groupers...

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Lampros Mouselimis

5 August 2024 9:58am

hi, if your intention is to use programming and a programming language like Python then one option which can give good results is the SAM (Segment Anything) or SAM-2 algorithm. The following weblinks include more information:

 

Larry O'Brien

17 August 2024 12:34am

Agreed. I have recently begun using SegmentAnything as a replacement for Detectron and have been very pleased. However, for a fish school I don't know how well it would do out of the box with the many overlapping fish. 

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discussion

Rapid Camera Trap labeling with ChatGPT

Sara Olsson

17 July 2024 3:19pm

Hi all, I've published a blog post on rapidly labeling camera trap data using ChatGPT for species identification and a simple object detection model to get the bounding boxes....

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Herdhanu Jayanto

20 July 2024 3:28pm

super interesting, thank you for sharing! definitely will watch!

Sarah Mshanga

3 August 2024 7:46pm

Really interesting, I will take a look

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discussion

WILDLABS AWARDS 2024 - Mobilizing Motus: optimizing a wildlife tracking data pipeline for aninternational, collaborative conservation technology community

Lucas Berrigan

13 July 2024 10:04pm

We’re delighted to introduce our project, Mobilizing Motus. Motus, a Latin word for movement, is a collaborative wildlife tracking system that uses automated radio telemetry...

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discussion

Simple Data Standards for wildlife reserve management scenarios?

HeinrichS

23 July 2024 7:16am

Hi - I've been lurking on Wildlabs for a while, consuming as much info as humanly possible, but I seem to miss specific info for my current needs.I'm the self appointed in house...

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Carly Batist

24 July 2024 5:48pm

Just as a note, you might also be interested in specific protected area management software like SMART or EarthRanger as well!

HeinrichS

25 July 2024 10:11am

Thanks!

I'm definitely looking at Smart and EarthRanger for overall management eventually, but for now I just want to track what we have better - especially as a base map to support further advanced management activities. Funding and available human resources to effectively manage a tech based scientific and best practice focused solution is in short supply - but will hopefully be better addressed within the next year or two. 

 

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discussion

Auto ID Software for NA Amphibians?

Cortney Dean

20 July 2024 3:57am

Hi All!So I'm currently running 4 Wildlife Acoustic Song Meter MiniBats at my beaver research and control sites as a means to measure species richness. 2 units at each site, one...

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Vanesa Reyes

24 July 2024 5:12pm

Hi Cortney,

I recommend exploring the tools developed by Kitzes Lab, such as OpenSoundscape, which can be used for the automatic detection of anurans. Here's a reference paper that might be useful. You might also consider reaching out directly to Justin Kitzes @jkitzes  for more specialized advice.
Also here is a another paper that use BirdNet to automatically detect the bullfrog presence.
Best of luck with your analyses!

Carly Batist

24 July 2024 6:15pm

Retweet on OpenSoundscape - great package and documentation that allows you to build your own CNNs! Note that this is in Python though. 

There are tons of bioacoustics software and packages in @tessa_rhinehart 's helpful list too! Some more recent options that I don't think are on that yet are Whombat and gibbonNetR (which uses the 'Torch for R' ecosystem). 

Also, Raven has template- and energy-based detectors you could try as well. The monitoR and warbleR packages allow you to do template-based detections too. BirdNET is integrated into Raven now as well.

You can also try Kaleidoscope's native clustering function.

Agree with you that there's definitely not enough resources for frog detection though! I'm assuming the Australian one you found is FrogID? There is also AnuraSet, but this is for neotropical frogs.  

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discussion

Move BON Development: Follow up discussion

Lacey Hughey

19 June 2024 12:02pm

Hey Biologging Community! We just launched a new initiative to mobilize animal tracking data in support of national and global scale conservation goals (learn more here!). If you...

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Akiba

12 July 2024 5:38am

Hi Talia! 

I feel like the topic is so broad that it might help to put some constraints around things, see what works, and then broaden those out. I have a lot of ideas regarding the data monitoring and collection side based on the other sensor and observation networks we've set up in the past. 

There may also be some potential scope to incorporate things like data collection and integrated monitoring to the Build Your Own Datalogger series where the system is updated to feed data into the observation network. 

It'd probably take a bit of discussion and coordination. Let me know if interested. I'm fine to jump on a call or discuss via email too.

CathyNj

22 July 2024 9:24pm

@cmwainaina please take a look

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discussion

Looking for literature materials/any useful data on HHC(Human-Hippopotamus Conflict) mitigation and coexistence.

Loveness L Mutungi

12 June 2024 7:24pm

Hello Wildlabbers,I am looking for anyone who have done some research on human-hippopotamus conflict mitigation and coexistence or anyone who might have some scientific info/...

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Nyangeta Magesa

7 July 2024 10:07am

Hi loveness,

Your doing great here are some research that may be helpful on what your looking for

search for article of Human-Hippopotamus Conflict: Impacts and Mitigation Strategies published in the Journal of Wildlife Management.

https://www.google.com/search?client=ubuntu-sn&sca_esv=23430e1df8f38b82&channel=fs&q=Assessing+Human-Wildlife+Conflict+with+Hippopotamuses+in+the+Context+of+Wildlife+Conservation+from+the+African+Journal+of+Ecology.&sa=X&ved=2ahUKEwigkNqHx5SHAxXi0gIHHaOBA-EQgwN6BAgFEAE

 

 

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Link

Rapid Camera Trap labeling with ChatGPT

Sara Olsson

17 July 2024 3:02pm

Hi all, I've published a blog post on rapidly labeling camera trap data using ChatGPT for species identification and a simple object detection model to get the bounding boxes. While presented in Edge Impulse, this approach can be replicated outside the platform using Python...

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careers

Data Manager, Conservation International

Esther Githinji

8 July 2024 2:40pm

Conservation International are seeking a data expert to help (a) serve as a day-to-day technical project manager to ensure data collection, data management, and data quality control with global program teams and...

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Link

EarthRanger: How high-tech tracking is keeping tabs on wildlife | CNN

Esther Githinji

5 July 2024 10:40am

EarthRanger use in Northern Kenya's Sera Conservancy by veterinarians to track and monitor rhinos.

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discussion

Question About Interpolation

Raul Castillo

18 June 2024 10:52pm

Hello! I am a Computer Science Student experimenting with the multi-step models on TensorFlow's "Time series forecasting" tutorial.I am applying to the models the positional data...

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Larry O'Brien

28 June 2024 6:35pm

The use of synthetic training data such as interpolated sequence values is common, but fraught with the issue of your synthetic signal generating features that are not true to real life. 

Instead, you might think about about appending the values of two long-period sin waves per input element to the sequence going in to your first linear / fully-connected layer. The simplest thing that could possibly work would be to interpret minute of the day and day of the month as the values of your sin wave! (Or perhaps minute/hour if all training sequences are quite short.) Since you’re doing sequence prediction, you would add the appropriate values for each image(?) in the sequence being evaluated.   

With that additional signal going in to the model in the early layers, the NN should have a good chance of learning that the differences in the modulating signal corresponds to distance in time. 

This technigue was popularized by early Large Language Models to encode the distance between words. There’s been refinement (search “Rotary Encoding” for instance) but the basic idea of sin waves generalizes well.

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discussion

'recurse' R package help

Zach Ng

17 June 2024 11:49pm

Hi all!  I am researching the spatio-temporal movements of reintroduced eagles, using the recurse package in R Software (developed by Bracis et al. - using the bird 'Leo...

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article

NEW PUBLICATION ALERT!

Consolata Gathoni Gitau

17 June 2024 11:33am

One of the most thrilling moments for any researcher is seeing their hard work published for the world to see. As part of the Women in Conservation Technology (WiCT) Kenya Cohort One, we not only learnt about the use of...

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Esther Githinji

17 June 2024 12:57pm

Congratulations Consolata!!! So exciting to read this :)
Sarah Maagi

17 June 2024 7:40pm

Many congratulation Consolata for such a milestone.
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