Sunday, September 25, 2022
HomeZoology BlogsScience Scribbler: Key2Cat Replace from Nanoparticle Selecting Workflow

Science Scribbler: Key2Cat Replace from Nanoparticle Selecting Workflow

Science Scribbler: Key2Cat Replace from Nanoparticle Selecting Workflow


That is the Science Scribbler Workforce with some thrilling information from our newest venture: Key2Cat! Now we have been blown away by the unbelievable assist of this group – a whole bunch of you’ve got taken half within the Key2Cat venture ( and helped to choose nanoparticles in our electron microscopy photos of catalyst nanoparticles. In simply 1 week, over 50,000 classifications have been accomplished on 10,000 topics and 170,000 nanoparticles and clusters have been discovered!

Thanks for this large effort!

We went by means of the info and ready every little thing for the subsequent step: classification. Getting the central coordinates of our nanoparticles and clusters with the proper class will permit us to enhance our deep studying strategy. However earlier than moving into the small print of the following steps, let’s recap what has been executed to this point utilizing the gold on germanium (Au/Ge) information for instance.


Within the first workflow, you have been requested to select each nanoparticles and clusters utilizing a marking instrument, which appeared one thing like this:

As you might need realized, every of the photographs was solely a small piece of an entire picture. We tiled the photographs in order that they wouldn’t be so overwhelming and time-consuming for a person volunteer to work with. We additionally in-built some overlap between the tiles in order that if a nanoparticle fell on the sting in a single picture, it will be within the centre in one other. Every tile was then proven to five completely different volunteers in order that we may kind a consensus on the centres of nanoparticles and clusters.


Along with your huge pace, the entire Au/Ge dataset (94 full dimension photos) was categorised in only a few days! Now we have collected your entire marks and sorted them into their corresponding tiles. If we contemplate only a single tile that has been checked out by 5 volunteers, that is what the output information appears like:

With some pondering and coding we are able to recombine all of the tiles that make up a single picture, together with the marks positioned by all volunteers that contributed to the picture:

Recontructed marked picture

Wow, you all are actually good at selecting out the catalyst particles! Seeing how exactly all centres have been picked out on this visualisation is kind of spectacular. You might discover that there are greater than 5 marks per nanoparticle – that is due to the overlap that we talked about earlier. When taking the overlap into consideration, because of this every nanoparticle needs to be seen (a minimum of partially!) by 20 volunteers.

The following step is to mix all the marks to discover a consensus centre level for every nanoparticle in order that we have now one set of coordinates to work with. There are quite a few methods of doing this. One of many first that has given us good outcomes is an unsupervised k-means algorithm [1]. This algorithm appears at all the marks on the picture and tries to search out clusters of marks which might be shut to one another. It then joins these marks up right into a single mark by discovering a weighted common of their placements. You may consider it like tug-of-war the place the algorithm finds the centre level as a result of extra marks are pulling it there.  

Reconstructed picture with centroids of marks

As you’ll be able to see, the consensus based mostly in your marks virtually completely factors on the centres of particular person nanoparticles or nanoparticle clusters. We don’t but know from this evaluation if the nanoparticle is part of a cluster or not, and in some instances, we additionally get marks in areas which aren’t nanoparticles as proven within the orange and purple containers above. Since solely small elements of the general picture have been proven within the marking activity, the artifact within the orange field was mistaken as a nanoparticle and within the case of the purple field, there’s a mark on the very edge and on a really small dot-like occasion the place a few of you might need been suspicious about one other nanoparticle. That is anticipated, particularly since we requested volunteers to put marks in the event that they have been not sure – we wished to seize all doable cases of nanoparticles on this first step!


That is the half the place the second workflow comes into play. Utilizing the marks from the primary workflow, we createda new dataset exhibiting only a small space across the mark to gather extra data.On this workflow we ask a couple of questions to assist establish precisely what we see at every of the marks

With this workflow, we hope to categorise all of the nanoparticles and clusters of each the Au/Ge and Pd/C catalyst methods, whereas potential false marks may be cleaned up! As soon as that is completed, we’ll have all of the required inputs to enhance our deep studying strategy.

We’re presently amassing classifications on the Au/Ge information and can quickly swap over to the Pd/C information, so you probably have a couple of spare minutes, we’d be very completely happy in the event you left some classifications in our venture!

-Kevin & Michele

Acquired your curiosity? Do you’ve got questions? Get in contact!



[1]: M. Ahmed, R. Seraj, S. M. S. Islam, Electronics (2020), 9 (8), 1295.



Please enter your comment!
Please enter your name here

Most Popular

Recent Comments