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Tutorial: Processing videos to assess
the time individuals spent at the
feederLilianasinternship
2014.02.26
Dominance and access to the foodresource
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Objectives
For two hoursof feeding per video maximum:
Record the time each individual spent in the periphery area =
OUT zone
Record the time each individual spent in the feeder area =IN zone
Record with a binomial variable (0 = feed on the edge; 1= feed
inside the feeder) whether each individual are feeding from
the edge of the feeder or from inside =Feed.in
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Zone IN
Zone OUT
This one feeds inside the IN zone and you will
have to write 1 in the feed.incolumn
because it is feeding inside the feeder
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Files and software
Download the latest version of VLC (free)
Open VA resource alim 2013-2014 _ L
Open the video you have to process with VLC
NOTES:1. If you cannot read the video smoothly from the hardware using VLC, you mayneed to copy the video first on your computer if this does not solve the pb,that means your graphic card is not powerful enough which means we willhave to find another computer
2. Try to be organized, keep track of videos you have processed already etcMaybe create an excel file where you list all the videos you have to analyze
and a variable showing if you did it or not It is also quite interesting to havewritten the bout of time where birds are seen at the feeder OR moreconvinient, the bout of time where no birds are around (it helps if we have tolook at the video again)
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VLC tips
Use the key - to slow down a playback
Use the key + to accelerate a playback
The more you press these keys, the
faster/slower the video is played.
Use the keyboard main tab to pause theplayback
When no bird are around, move the cursorforward from about 10s (not more otherwiseyou may miss things)
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Before you press the start button
From file: VA resource alim 2013-2014 _ L
Enter year, month, day, col, processor (= your initial)
time start, time end, duration of the video (if less than 2hrs,
note it and process the video until the end, if > 2hrs, do only 2hrs: its painfulenough!).
Have a look at my behavioural observation file
to extract the ID of the birds I have observed
around. It will facilitate the ID determination from thevideoFilter per colony
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How to write colour IDs
BK = BLACK
DB = DARK BLUE
EG = EMERALD GREEN
FP = FLUO PINK LB = LIGHT BLUE
LG = LIGHT GREEN
OR = ORANGE
PS = PINK STRIPE (black bandwith fluo-pink stripes)
RE = RED
VI = VIOLET
WH = WHITE
WS = WHITE STIPE (black
band with white stripes) YE = YELLOW
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How to write colour IDs
Colour IDs have to bewritten with the followingorder
Upper left; Lower left; upperright; lower right
Left hand side is the left leg of thebird (on the left when you look at the
back of the bird)For instance: the bird on the pic isYEWHYEM
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How to write colour IDs
One more example:
This one is WHREYEM
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How to write ID with missing ring
UR = Code for missing ring (UnRing)
If the colour ring above the metal ring is
missing, always write URM
If one colour is missing from the leg with no
metal ring, always write the color code first
ORUR or DBUR or REUR or LBUR etc
Example: ORURURM has one colour missing and one orange
band on the left hand side and just a metal ring on the right
hand side.
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For example:
This one is
EGURYEM
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Be aware of
Light Blue (LB) and White (WH) are very very
tricky, hard to differentiate on videos, make sureyou do not have birds that differ only from those colours. If it is the case
and you have trouble, email/skype me (i.e. at colony 27 there are a
LBORORM and a WHORORM)
DB and BK can also be a bit tricky when the light is notgood but usually, the exposure change and the confusion vanishes
Be very careful not to omit any time and toenter time correctly
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For example:
This one is
LBLBYEM and not
WHWHYEM luckily,in that colony there is no
WHWHYEM so it makes
thing easier
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With the next slides, I have attempted todescribe you as best as possible how I proceedto process a video (so what you should do!)
In that example, we are looking at whathappens from 1hr 08 min 15 sec after westarted the camera & positioned the feederunder the colony
To simplify, I used A,B,C,D,E,F instead ofColour IDs
Example of video processing
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Example of video processing
A
B
CE
D
F
1h08m15s
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Yr Mth Day Col Proc
.
AM/
PM
IN/
OUT
ID.
Col
Start End Duration Total
Video
Fee
d.in
2013 09 9 33 MR PM OUT A 1:06:09 02:00:00
2013 09 9 33 MR PM OUT B 1:07:52 02:00:00
2013 09 9 33 MR PM OUT D 1:08:02 02:00:00
2013 09 9 33 MR PM OUT E 1:07:08 02:00:00
2013 09 9 33 MR PM OUT F 1:02:05 02:00:00
2013 09 9 33 MR PM OUT C 1:08:01 02:00:00
2013 09 9 33 MR PM IN A 1:08:10 02:00:00 1
2013 09 9 33 MR PM IN B 1:08:12 02:00:00
2013 09 9 33 MR PM IN D 1:08:07 02:00:00
1. A few seconds before 1:08:15, these 6 individuals were all in the OUT zone. A,B,D,E,F,E
jumped over the green hoop and stayed at least 2 sec in the OUT zone therefore we
enter for each of them at what time they entered the OUT zone, we specified it is the
OUT zone considered here and we precise the ID.
The table should look like the one above
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Example of video processing
A
B
CE
D
F
1h08m15s
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Yr Mth Day Col Proc
.
AM/
PM
IN/
OUT
ID.
Col
Start End Duration Total
Video
Fee
d.in
2013 09 9 33 MR PM OUT A 1:06:09 1:08:10 =End-Start 02:00:00
2013 09 9 33 MR PM OUT B 1:07:52 1:08:12 00:00:20 02:00:00
2013 09 9 33 MR PM OUT D 1:08:02 1:08:07 00:00:05 02:00:00
2013 09 9 33 MR PM OUT E 1:07:08 02:00:00
2013 09 9 33 MR PM OUT F 1:02:05 02:00:00
2013 09 9 33 MR PM OUT C 1:08:01 02:00:00
2013 09 9 33 MR PM IN A 1:08:10 02:00:00 1
2013 09 9 33 MR PM IN B 1:08:12 02:00:00
2013 09 9 33 MR PM IN D 1:08:07 02:00:00
2. But then individuals A,B,D leaves the OUT zone (at respectively 1:08:10, 1:08:12 and
1:08:07 to start feeding directly from the feeder, standing on the edge for B,D. In the middle
of the feeder for A Enter the time they left the OUT zone inside the End column for each individual.
Use these times as a Start time for the IN zone for each of those 3 individuals
Also, individual A is feeding inside the feeder so do not forget to write 1 in the feed.in
column.
Careful, it is very easy to forget a End time, always check that the number of birds you
see in each zone (IN and OUT correspond to the data entry with no End time yet.
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A
B
CE
D
F
1h08m29s
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Yr Mth Day Col Proc
.
AM/
PM
IN/
OUT
ID.
Col
Start End Duration Total
Video
Fee
d.in
2013 09 9 33 MR PM OUT A 1:06:09 1:08:10 =End-Start 02:00:00
2013 09 9 33 MR PM OUT B 1:07:52 1:08:12 00:00:20 02:00:00
2013 09 9 33 MR PM OUT D 1:08:02 1:08:07 00:00:05 02:00:00
2013 09 9 33 MR PM OUT E 1:07:08 02:00:00
2013 09 9 33 MR PM OUT F 1:02:05 02:00:00
2013 09 9 33 MR PM OUT C 1:08:01 02:00:00
2013 09 9 33 MR PM IN A 1:08:10 02:00:00 1
2013 09 9 33 MR PM IN B 1:08:12 02:00:00
2013 09 9 33 MR PM IN D 1:08:07 1:08:29 02:00:00
2013 09 9 33 MR PM OUT D 1:08:29
3. At 1:08:29
A, B are still in the IN zone
D left the IN zone, we need to create a new OUT entry
C, E, F, are still in the OUT zone.
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1h08m37s
A
B
CE
D
F
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FA
C
B
D
1h09m17s
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5. At 1:09:17
A is still in the IN zone (he may not be inside the feeder anymore but as he went at
least feeding from inside once during this bout, we keep the variable 1)
C is still in the OUT zone
D is still in the IN zone but went inside the feedertype 1 in the feed.in column
E left the OUT zone and the whole feeding areaenter End time in the OUT entry
for this ind.
F left the OUT zone to feed in the IN zone from the edge.enter End time in
the OUT entry and create a new IN entry with this same time for this ind.
B left the IN zone to feed in the OUT zoneenter End time in the IN entry and
create a new OUT entry with this same time for this ind.
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Yr Mth Day Col Proc
.
AM/
PM
IN/
OUT
ID.
Col
Start End Duration Total
Video
Fee
d.in
2013 09 9 33 MR PM OUT A 1:06:09 1:08:10 =End-Start 02:00:00
2013 09 9 33 MR PM OUT B 1:07:52 1:08:12 00:00:20 02:00:00
2013 09 9 33 MR PM OUT D 1:08:02 1:08:07 00:00:05 02:00:00
2013 09 9 33 MR PM OUT E 1:07:08 1:09:17 00:00:09 02:00:00
2013 09 9 33 MR PM OUT F 1:02:05 1:09:17 00:07:12 02:00:00
2013 09 9 33 MR PM OUT C 1:08:01 02:00:00
2013 09 9 33 MR PM IN A 1:08:10 02:00:00 1
2013 09 9 33 MR PM IN B 1:08:12 1:09:17 00:01:05 02:00:00
2013 09 9 33 MR PM IN D 1:08:07 1:08:29 00:00:22 02:00:00
2013 09 9 33 MR PM OUT D 1:08:29 1:08:37 00:00:08 02:00:00
2013 09 9 33 MR PM IN D 1:08:37 02:00:00 1
2013 09 9 33 MR PM IN F 1:09:17 02:00:00
2013 09 9 33 MR PM OUT B 1:09:17 02:00:00
Check:
We have 3 birds that are supposed to be still in the IN zoneYES
We have 2 birds that are supposed to be in the OUT zone
YES
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More rules
Suppose individual E comes back to the OUT zone jumping over the
hoop and then crossing the OUT zone quickly to directly reach the IN
zone It is quite time consuming to create new row/entry for such
behaviour So if a bird stays < 2 sec in a zone, do not create a new entry
for that zone. Use the time the ind enters/leaves the first zone it crossed
as a start time.
Another rule, sometime they move from the edge just for a bit and come
back to the feeder, if this is < 2 sec, do not end the IN entry to create a
new OUT entry and then again a new IN entry
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General advices
BE PATIENT! Do not rush this analysis otherwise it is prone to
mistakes! And we need accurate data!
I know it can be painful, believe me, I am doing very intense videos at the moment for
which I can spend sometime 15min processing 1min of video because there are a lot
of movements between zones and a lot of birds! I have been as kind to you as possible
and I have spared you the most intense colonies!
When they are many birds at the same time, I found
sometime easier just to follow one bird (i.e. focal obs) at the
time for that crazy bout and then play the bout again andfocus on a second bird
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General advices
When your eyes start to be very red, your
brain painful and your nerves at the edge of a
breakdown Sit back, breath, relax, enjoy a
coffeetake a break and come back to itonce youve calm down
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Priorities
Start by colony 21 and colony 81
I will send you a list of 5 video ID for each
colony. You will start with those, then
probably 5 more. That means you will have
to analyze 20 videos of 2 hours
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Good luck!!!!!!!!!!!!!!!
If you have any questions
[email protected] I am usually on
skype for emergency (username: margaux.rat)
mailto:[email protected]:[email protected]