EVE General Discussion

Im pretty sure you selected the correct one... its just gonna take time for people to get good at this, and for the system to weed out the bad ones =p



was i was right in selecting the two categories for this one? Previously i was only selecting Nucleus on samples like this because i felt it was the prominent feature, but now as ive went though some of these and getting more comfortable, im thinking this should be both Nucleus and Cytoplasm?
http://i.imgur.com/iYVeStn.png

I went with Cytoplasm and not Vesicles because the staining in the red part was more blurry, not really defined dots


Im also curious what the difference between an "Abnormal sample" and "cell to cell variation"/"not identifiable" would be

http://i.imgur.com/tkkrx53.png Try and work that one out for a laugh.

Could be mitochondria or a golgi apparatus? I think it's something on top of the nucleus (the red filaments running through the nucleus are a giveaway), not actually in it.

The new feature has caused many inconsistent results. Especialy with basic findings where you are 100% accurate but get a failed result. This has baffled me if I should continue wasting my time in project failure.

For starters the pictures should be increased in size instead of looking through a key hole.

Can we get 3d images if possible.

Why did I fail with one of the results. Please give back users more explanatory information to educate them more on failed results instead of guessing.


I like to help like many others though I believe the new feature needs to be expanded with more features. At this stage until I see improvement I won't be committed to it as I once thought.

The examples are only showing 1 location, to make it easier to see what it should look like. However, most images (>60%) will have at least dual (some triple) locations, and nucleus/nucleoplasm + cytoplasm is the most common one by far.

In this one I wouldn't click cytoplasm though, but that's based on that it's so weak, that I don't believe it's a specific staining (but it's borderline, so as a gamer, I think you probably should :))

I think (not sure) that there's a forum thread that's better for giving feedback regarding the UX/UI. I'll ask ppl to have a look in this forum too though.

3D images is not possible atm as we've so far only acquired 2D images. The reason is that taking 3D just takes too much time (atm 1 image takes around 3s by the microscope, just the actual acquisition, if it were to be 3D it would be a minute or so... that times 150k samples = no doable, unfortunately. It would be awesome to have though!).

Well I do science all day, and then come home to fly spaceships and blow stuff up and end up doing science again. It never ends!!

Thanks for elaborating, it's interesting to hear what ppl think! I agree that accuracy is really important. NB that each images is of a focal plane/narrow slice of the cell, so for something to be seen from "outside" of the slice, it has to be a reaaaally strong staining, or the image is acquired at the interface between nucleus/cytoplasm.

What we do now is rather than acquiring 3D images, if something can't be visualized perfectly in one image, we will take several images of the same cells, but at different focal planes. That way we can vizualise e.g. focal adhesions in one image, and in the next we will show e.g. nuclear speckles. But yes, it would be ideal to have high-res 3D images to scroll through.

If you see spots in the blue area, and when toggling on/off the red, you see a nice outline of the cell w/o any red in the blue parts - then you know that the image you look at have been acuired "in the middle" of the cell. Thus, the spots in the blue should be there, rather then floating below/on top. Also, the look of the spots can usually tell whether they are in focus or not. If they are big (subjective, I know) and somewhat blurry, they aren't in focus, and you should be hesitant. If more distinct, they are in the same focal plane as the nuclei, and you can trust them.

Technical comment:

No, we acquire 2D images (Leica SP5 confocal microscopes). We have the possibility of acquiring 3D images in the form of stacks, i.e. that the mic first images a slice at the bottom and then works its way up to the top of the cell, slice by slice (the number of slices can be set manually). The reason for using this kind of microscopy is that it gives high-resolution images, and we can look at a certain focal plane at the time (compared to a microscope that images the whole cell at the time, but at much worse resolution). High-res images are really necessary to see substructures such as e.g. the centrosome or fibrillar center. Each focal plane (slice) is very narrow, so (as I mentioned above) for something to be seen from below/above, the signal from it either has to be really strong, or the slice has to be in close proximity to e.g. the interface between the nucleus and cytoplasm.

The reason that it's so time consuming to do image acquisition is that the microscope scans with 1 laser over the sample, then the 2nd laser and finally the 3rd (exciting the fluorophores in the sample at different wavelengths. We have to excite separately to avoid bleedthrough between different channels, eg that staining in the blue is seen in green etc).

Also, the resolution in z will not be as good as the one in xy 2D (general thing due to some laws of physics/how light move through different media or smt that I would have to refresh my memories on before commenting on), which means that even if we do 3D images, they won't be perfect.

Sorry for nerding out on microscopes :)

I'll actually ask my colleague HPA_Dichroic to give some input on this, as he's working with image analysis and could comment so much better.

Thanks for discussing & coming with ideas, love the interest from everyone!

A quick question on the cell-to-cell variation option, how much does it play into the weighting of your accuracy change if you tick cell-to-cell variation but others haven't, or if you don't tick it and others have? Is it treated just like the other answers?

The reason I am asking is that a lot of the time, this box doesn't seem to be being ticked by the majority for some obvious variation so the consensus has it at 0. I guess this is also even more subjective than the other classifications as it comes down to how much variation justifies ticking the option.