Sample data

Experiment 1:

Links fixed and OSF repository made public 4Oct18.

Adult C. elegans, alive vs dead. Approx 3 frames per second. Column labels are in the images. Note that the plates are rotates 90 degrees CW in the images.

Columns 1 and 2 contain live adult worms and eggs

Columns 3 and 4 contain 50% live worm sample, 50% dead worm sample by volume

Columns 5 and 6 contain dead worms. Eggs in these samples were present before killing.

Worms were killed by two cycles  of freezing for 20 minutes and thawing.

Please note that it is very difficult to kill worms without causing mechanical damage. Many nematicidal compounds cause a paralysis and worms frequently recover once the nematicidal agent is washed away. Also note that we have observed paralysis of worms in various conformations (straight, curved, coiled etc), so paralysis not as straightforward a phenotype as people often imagine.

Images for this experiment are here (moved to OSF).

Experiment 2:

Time course of paralysis under aldicarb treatment. Aldicarb is a pesticide, formerly in widespread agricultural use, that causes paralysis of adult C. elegans. Conveniently, aldicarb also stimulates egg-laying. Therefore, over the course of this experiment, you should be able to observe two chemically-induced phenotypes:

  1. Increasing paralysis
  2. Increasing egg count

I have included seven different doses of aldicarb and a negative control, each in 6 replicate wells:

A1:A6    8 mM Aldicarb,

B1:B6    6 mM Aldicarb

C1:C6    4 mM Aldicarb

D1:D6    2 mM Aldicarb

E1:E6    1 mM Aldicarb

F1:F6    0.5 mM Aldicarb

G1:G6    0.25mM Aldicarb

H1:H6    No aldicarb: negative control.

I captured this experiment at 1 sample per minute for 3 hours, to give you some appreciation of the timescales over which most events occur in this assay. We would gather much less data for a screening experiment. Here, “a sample” is composed of two images, separated by a 500 ms interval. By comparing each pair of images (<sample_number>.tif and <sample_number>b.tif), we can derive a movement score.

The raw image series is here. For your convenience, I have provided a numpy array describing the coordinates of well centres here.

Here is a plot of our simple movement scores, note that I would normally calculate these scores live, during experiment runtime:

ald_adult

There is a numpy array containing this data here (well A1 is at index [0,0,t], well H6 is at [7, 5, t]. I have included our movement data images here; blue denotes invariant pixels, green denotes changed pixels between the two successive images. For these movement data images, there is a single image for each timepoint, containing movement information derived from the two successive images in the raw data.

File index:

Adult worms, Alive, dead, 50/50. 26 images over 10 seconds

Adult worms, aldicarb titration. Two images at 500ms separation, sampled every minute for 3 hours.

Adult worms, aldicarb titration. Movement score images, every minute for 3 hours

Adult worms, movement score data (numpy array)

Well centre coordinates for aldicarb experiment