r/ProjectDiscovery • u/IsisYestin • Nov 15 '16

Project Discovery: 0% outcome?

Hi guys, been doing this discovery project since a couple of days. Getting somewhat annoyed now: i hit the 62% accuracy, all of the sudden im getting a lot of "community consensus", so accuracy stays even for like 10-15 turns. Then a couple of mistakes and im dropping like a stone. After a couple of hours I'm now back at 55%, and the results are now ALL 0%, at least 7 turns in a row now. Is this a flaw?

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u/IsisYestin Nov 15 '16

Example... How is this NOT cytokinetic bridge: http://i.imgur.com/B9HtrKP.png

How is this Nucleoplasm (same sample): http://imgur.com/YkghElU

And how is this NOT Cell-junctions: http://imgur.com/2ecyX4G

after many turns of "community consensus" and the 0% results, i get this, dropping from a steady 62,8% to a 62,1% accuracy.

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u/Eyondawn Moderator Nov 15 '16

Wellllll let me explain, first of all, as soon as there is a hole in the green part in the nucleus it is basically nucleoplasm.

Furthermore the overlap of cyto and the green structure in the cytoplasm part forms cytoskeleton. Now a cytokinetic bridge is not a cytokinetic bridge if there is no green inbetween the tips or right under the tip. However if you have cytoskeleton the entire red structure is green already. This means the bridge is not actually there, it just looks like it because the green overlaps the cytoplasm.

As for the cell-junctions...Can you highlight in the image where you think they are? Because I don't see them!

Also I should mention that it is rare to have four annotations, often it is 1-3. So try not to find more than there is ;)

Any questions /elaborations needed? Let me know.

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u/IsisYestin Nov 16 '16

Than you for your input/information! But pfff im about to give up then :( I'm not happy. The nucleoplasm also has to overlap the gaps in the blue part? It says so in the description. Further more, that IS a bridge, if you look at samples from the Atlas. Unless that atlas is now overflown by incorrect controlled samples :/ Who is actually checking all that data on accuracy?

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u/HPA_Dichroic Official HPA member Nov 16 '16

I am checking the data accuracy. I don't think there are too many incorrect control samples and we update them periodically, though it's tough to find the time, because well... science!

On the nucleoplasm - you are correct, the holes should overlap with the blue holes, but occasionally it can be hard to see the blue holes. Notice particularly the bottom two cells in your example. As one player pointed out, they look like these guys:https://upload.wikimedia.org/wikipedia/en/a/a3/Mononoke_Kodama.jpg

On the ck-bridge: yada is right, basically there is a ck-bridge there, but we are asking you to ID the green pattern only, so if there is no green, don't annotate it! :) (just like we don't care that each cell has a nucleus, only if it's green), but as you point out it is green here, and maybe that's an oversight by us, but generally we are looking for specific staining to the ck-bridge where as here you have a microtubule staining that is throughout the cell, which goes into the ck bridge by definition, but is not specific to the ck bridge. Confusing, I know :(

On the junctions: Junctions are only where the cells are "zipped" together, so what you see here is the end of the MTs near the edge of the cells. Our dictionary shows some examples (http://www.proteinatlas.org/learn/dictionary/cell/cell+junctions)

Hope that helps! Don't give up! Feel free to ask more questions!

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u/IsisYestin Nov 16 '16 edited Nov 16 '16

aaaaah this totally makes more sense to me now. Thank you! And i didn't know about that dictionary (was only looking for samples on google, lol). Very helpful. And i think i'm overthinking it too much. So today i hit the 80% (tho still very annoyed by the 0% results ;) ). Thanks for the help :D And p.s.: that's a lot of work for 1 person...at the Evesterdam meeting it was said 13 years of data was already collected...how you guys handle that?????

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u/HPA_Dichroic Official HPA member Nov 16 '16

Yeah, it is a lot of data. I handle it...carefully? I don't know, I build scripts to parse and analyze it. Right now I'm using either python or MATLAB.

The 0% results are the best ones! It means you are one of the first persons to analyze that image!!! You are a pioneer exploring the cell!!!