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Project Discovery: Challenging & Interesting Samples

First post
Author
HPA Illuminator
H P A
C C P Alliance
#141 - 2016-04-01 10:47:02 UTC
Memphis Baas wrote:
Why is the nucleus option wrong in this accuracy sample?
http://imgur.com/SjyQSxW

Please explain.


Hm, do I understand it right that the classification was supposed to be nucleoplasm+ER? That's odd, because it should only be ER. I've submitted it to have the nuc removed (and add variations).

It should only be ER as the weak nuclear staining that can be seen is due to background bleedthrough from ER below the nucleus. The green in the nucleus is way to weak to be a true nuclear staining.
HPA Illuminator
H P A
C C P Alliance
#142 - 2016-04-01 10:48:46 UTC
Yllej Gniht wrote:
Image no. 100000325

Classification Result says: "Nuclear Speckles"; it sure looks like "Nucleoplasm" to me.

What's the deal here? Is this faint variation enough to declassify it as "nucleoplasm" and flag it as "nuclear speckles"?

If so, some explaining text would be appreciated with those very hard to understand "teaching moments".

Thank you! :)


This is also one of the known errors, it should indeed be nucleoplasm and nuclear speckles (at first we thought they were mutually exclusive, which is why this one happened). It will be corrected asap.
HPA Illuminator
H P A
C C P Alliance
#143 - 2016-04-01 10:51:09 UTC
Cyndrogen wrote:
I just got a really weird sample.... at first glance it looks obvious but then it doesn't really fit into any category 100%

http://imgur.com/Wi6KjrS


more detail
http://imgur.com/BMsSyd1


Nucleoplasm for sure, and probably cytoplasm too. Or what part do you think was confusing?
HPA Illuminator
H P A
C C P Alliance
#144 - 2016-04-01 10:54:05 UTC
Joe Thelere wrote:
I had an image analysed by a professional today:
http://imgur.com/8cy3D7m
How much difference in intensity is needed to be correct with Cell-to-Cell-Variations? Or was the professional wrong?


I would be hesitant to call that variation as all strongly stained cells are in the bottom left part of the image. That makes me think it's possible (likely) that the plate was not perfectly adjusted when imaging, and that the cells were imaged at different focal planes, e.g. the stronger green ones were imaged more in the middle of the nucleus, making the staining appear stronger, and the weaker ones at higher up/lower > making the staining appear less strong.

HPA Illuminator
H P A
C C P Alliance
#145 - 2016-04-01 10:58:50 UTC
Circumstantial Evidence wrote:
Sample 100000440 has been defined as 100% Vesicles, and I regret not making this choice, in addition to Rods and Rings. I picked R&R because I saw a few rod-like structures... am I completely wrong, or could this sample contain both R&R and Vesicles? Must complete ring structures be present, in samples with R&R? I've marked the BG views with arrows.

Area 1 BG -- RGB || Area 2 BG -- RGB


Sample 100000264 has been defined as 100% Cytoplasm, but I wonder what the structures that seem to outline some parts of the cells might be, marked with arrows in my Green-only screenshot. I thought they might represent a plasma membrane.

100000264 Green -- 100000264 RGB


The first image was a really tricky sample, and I agree it kinda looks like R&R, but not really. Some type of vesicles have this elongated pattern that you can see here. We'll try to remove it from the training set.

For the second image, I see what you mean, but I don't think it's plasma membrane. The cells you look at is a type of brain cell (called U-251 MG), which is known for having what (at least we call) "membrane blebbing", which is that kind of thick edge at the membrane. If you toggle red/green on off you'd likely see a good overlap of the red/green, although the red might be weaker there.
HPA Illuminator
H P A
C C P Alliance
#146 - 2016-04-01 11:02:40 UTC  |  Edited by: HPA Illuminator
Selphentine wrote:
http://i.imgur.com/1jGFchx.jpg

Im by far noone that claims professionals are wrong, and i understand a lot of me seeing not the right things in PD, but im very, very sure that nucleoli shouldnt be wrong here.


Thanks for noticing, will be fixed!

Edit: So weird, when I check the image, it does show a nucleus, not nucleoli as in your image. Might have loaded the wrong image for some reason?
Joe Thelere
The fun part
#147 - 2016-04-01 11:41:30 UTC
HPA Illuminator wrote:
Joe Thelere wrote:
I had an image analysed by a professional today:
http://imgur.com/8cy3D7m
How much difference in intensity is needed to be correct with Cell-to-Cell-Variations? Or was the professional wrong?


I would be hesitant to call that variation as all strongly stained cells are in the bottom left part of the image. That makes me think it's possible (likely) that the plate was not perfectly adjusted when imaging, and that the cells were imaged at different focal planes, e.g. the stronger green ones were imaged more in the middle of the nucleus, making the staining appear stronger, and the weaker ones at higher up/lower > making the staining appear less strong.



Thanks for the explanation.

But for me it raises a problem: How can I decide if the visible varaitions in the staining are a result of the technical imaging-process or the staining itself?
HPA Illuminator
H P A
C C P Alliance
#148 - 2016-04-01 11:53:56 UTC  |  Edited by: HPA Illuminator
Joe Thelere wrote:
HPA Illuminator wrote:
Joe Thelere wrote:
I had an image analysed by a professional today:
http://imgur.com/8cy3D7m
How much difference in intensity is needed to be correct with Cell-to-Cell-Variations? Or was the professional wrong?


I would be hesitant to call that variation as all strongly stained cells are in the bottom left part of the image. That makes me think it's possible (likely) that the plate was not perfectly adjusted when imaging, and that the cells were imaged at different focal planes, e.g. the stronger green ones were imaged more in the middle of the nucleus, making the staining appear stronger, and the weaker ones at higher up/lower > making the staining appear less strong.



Thanks for the explanation.

But for me it raises a problem: How can I decide if the visible varaitions in the staining are a result of the technical imaging-process or the staining itself?


If you see a certain variation pattern only in part of the image, I wouldn't trust it. But, for the image you posted, if there had been a strong nucleus in eg upper right corner, it would be much more trustworthy. You can also turn on the red to see whether it looks similar for all cells - are the cells looking ok, or do some have granular red pattern, or look weird in some way? (>> don't trust them). By using the red channel you can also more easily tell whether the focal plane for the different cells seems to be similar.

For other variation patterns, eg if you have nucleus + nucleoli in lower left part of the image, but only nucleus for the rest, I would classify it as variations (as long as it's more than 1 cell - "1 cell is no cell") as it could be that very few cells show that variation, or that the difference in focal plane makes the nucleoli not visible in part ot the image.

Does it make more sense?
Svarii
Acclimatization
#149 - 2016-04-02 04:19:51 UTC
Test Sample#: 100000406

Why is the cytokinetic bridge option wrong on this sample?
It doesn't look wrong...

Test Sample # 100000406: http://i.imgur.com/Y3sUHSH.png
cytokinetic bridge circled: http://i.imgur.com/ZIbexUa.png

I don't mind my accuracy going down (or not going up) if I screw it up, but not when I'm right.
Can someone explain to me why cytokinetic bridge is not a correct answer here?
Galaxxis
Unicorn Rampage
#150 - 2016-04-02 04:37:55 UTC
Svarii wrote:
Test Sample#: 100000406

Why is the cytokinetic bridge option wrong on this sample?
It doesn't look wrong...

Test Sample # 100000406: http://i.imgur.com/Y3sUHSH.png
cytokinetic bridge circled: http://i.imgur.com/ZIbexUa.png

I don't mind my accuracy going down (or not going up) if I screw it up, but not when I'm right.
Can someone explain to me why cytokinetic bridge is not a correct answer here?


There is a great cytokinetic bridge there!! However it isn't glowing green and that's what you're looking for. They use dye that bonds to different parts of the cell, so don't pick something if it isn't bright green.
Svarii
Acclimatization
#151 - 2016-04-02 05:39:13 UTC
Galaxxis wrote:
Svarii wrote:
Test Sample#: 100000406

Why is the cytokinetic bridge option wrong on this sample?
It doesn't look wrong...

Test Sample # 100000406: http://i.imgur.com/Y3sUHSH.png
cytokinetic bridge circled: http://i.imgur.com/ZIbexUa.png

I don't mind my accuracy going down (or not going up) if I screw it up, but not when I'm right.
Can someone explain to me why cytokinetic bridge is not a correct answer here?


There is a great cytokinetic bridge there!! However it isn't glowing green and that's what you're looking for. They use dye that bonds to different parts of the cell, so don't pick something if it isn't bright green.


Okay, I see it now. The example is a bit yellow because of the green staining while the cytokinetic bridge I saw is just red since it's not stained at all.

Thanks!
Cytherea Deesse
University of Caille
Gallente Federation
#152 - 2016-04-02 10:22:27 UTC
I'm unsure if this is a cytokinetic bridge the green dots in the red marker cause the few times I have gotten cytokinetic it has been bright red bridges.

http://imgur.com/BMWZyoo

Tisiphone Dira
Garoun Investment Bank
Gallente Federation
#153 - 2016-04-02 10:56:17 UTC  |  Edited by: Tisiphone Dira
A rather odd cell

e: Oh and thank you project discovery for helping me realize my dream of crafting the most beautiful character in all new eden.

There once was a ganker named tisi

A stunningly beautiful missy

To gank a gross miner

There is nothing finer, cept when they get all pissy

Galaxxis
Unicorn Rampage
#154 - 2016-04-02 20:40:03 UTC
Tisiphone Dira wrote:
A rather odd cell

e: Oh and thank you project discovery for helping me realize my dream of crafting the most beautiful character in all new eden.


It's smiling at us. Back away slowly...

Also, you look like you were stitched together from a zombie's butt skin!!
Galaxxis
Unicorn Rampage
#155 - 2016-04-02 20:42:39 UTC
Cytherea Deesse wrote:
I'm unsure if this is a cytokinetic bridge the green dots in the red marker cause the few times I have gotten cytokinetic it has been bright red bridges.

http://imgur.com/BMWZyoo



I'm pretty sure it's cytokinetic bridge, since there are two of them both with that same green glob of ink. Not sure why it would look like that.
Sp3ktr3
Unicorn Rampage
#156 - 2016-04-11 04:43:46 UTC
Found it.
Kitty Bear
Deep Core Mining Inc.
Caldari State
#157 - 2016-04-11 12:31:10 UTC
It's all just coloured blobs to me ..

Raven Dallacort
The Scope
Gallente Federation
#158 - 2016-04-11 16:33:09 UTC
I think there's an error on the classification for your control sample.

http://i.imgur.com/pWNR1bC.png

Thanks for your time.
Elyia Suze Nagala
Republic Military School
Minmatar Republic
#159 - 2016-04-12 11:46:35 UTC
I have no idea how some people are selecting a few of their answers in PD. It's annoying because I'll select features that are very clearly present, but no one else selected that feature type and I then get dinged a few pecent. I'm like WTH?

I still like the idea of PD but it's annoying my ratings are affected because others aren't thorough.
ISD Max Trix
ISD Community Communications Liaisons
#160 - 2016-04-12 12:13:54 UTC
I've Stickied this thread. Keep Up the good work.

ISD Max Trix

Lieutenant

Community Communication Liaisons (CCLs)

Interstellar Services Department

I do not respond to EVE mails about forum moderation.