GSoC 2021 Project Idea 20.2: Brainbox projects - Brain Histology Metadata DB: Building an online database for storing, curating and sharing metadata from diverse collections of histological data

Problem: Brain histology provides unique information on the cellular structure of the brain. Histological data has been collected for more than a century, and is available for a wide variety of species and developmental stages. The physical slides require lots of effort for being digitised at high resolution, and thus, usually only selected slides, representing only specific regions and specimens within much larger collections have been scanned by individual researchers for their own projects. This has led to a wealth of digitised histological data being spread across several researchers and labs, with no coherent structure, common identifiers, or a method to see, access, and annotate the data.

Histological data is challenging to visualise, analyse and share, and often requires time intense manual curation and annotation. With the lack of a shared database, researchers find themselves redoing manual annotations redundantly, instead of being able to build an increasingly detailed picture of the brain microstructure together.

Vision: We would like to build an online database for storing, curating, sharing, accessing, and annotating metadata from several brain histology datasets, alongside with the real digitised data (images and text) whenever it is available. In a joint effort with anatomists worldwide we will build a searchable database for the primates of the Stephan and Zilles Collection, one of the most important histological data collections for comparative neuroanatomy. It represents the world’s largest collection of whole brain histological slides from diverse primate species, as well as other animals. We would like to make this data available to the scientific community in a structured way in order to reduce redundant efforts, allow scientists to tackle analyses and challenges collaboratively in a coordinated fashion.

Aim: We have access to records from different histological collections. The aim of the project will be to organise the data, develop a database, a RESTful API to query the data programmatically, and a Web interface to allow researchers to browse and query the database. Whenever digitised histological data becomes available, it will be made available with a link to our tool MicroDraw to visualise it and segment it collaboratively.

Scope: Create a database, API and UI for metadata on brain histology collections.

Skills needed: Javascript, Nodejs, Vuejs, HTML, CSS, MongoDB, RESTful API.

Lead mentor: Alexandra de Sousa.

Co-mentors: Katja Heuer & Roberto Toro.

1 Like

Hello Alexandra de Sousa,Katja Heuer @katjaq & Roberto Toro @rto

I’m Chetanya Tomar,3rd year B.tech Student from Computer Science Engineering at B.I.E.T Jhansi.My skill set consists of HTML,CSS,Javascript,AWS(beginner),React.js,Node,js,Mongodb and javascript and would like to contribute to this community and also willing to participate in GSOC’21 through this project.
It would be a great help to me if you could guide me how to start with this project and I’ve already read the necessary documents which were given in the projects post.
If you could set-up a google-meet regarding this project anytime favourable to you ,then it would be a great help to me as well as to all the people who are willing to contribute to this project.

1 Like

@arnab1896 ,can you please guide me for this project or the ways to be able to connect with the mentors regarding the project?

@chetanya_tomar , yup, let me notify the mentors. Will get back to you soon. Cheers!

2 Likes

Alexandra de Sous, @katjaq, @rto

Hello everyone! I’m Saarah from India currently doing a Masters of Technology in Computer Science at MSRIT, India. I’m excited and look forward to contributing and being valuable to INCF’s cause of open and FAIR neuroscience. This happens to be one of the two ideas which I feel passionate about at INCF and would be joyed to make beneficial contributions to!

Having worked on and built several end-to-end applications through my undergrad years with the tech stack mentioned alongside the problem statement, I believe my skill set could be useful in building this invaluable database! Having just finished an advanced data modelling and design course this semester, I would be elated to make beneficial contributions with the knowledge I’ve sought and continue to seek.

I would be grateful if I could be guided on how to start contributing to and building this project or any steps/guidelines I could take to be useful to INCF as of the moment. I would be happy to build a general application skeleton that could be made more specific later. Any advice to better make my case would be greatly appreciated.

Have a great day!

1 Like

Hello @chetanya_tomar , hello @Saarah_Asad ,

How nice to read from you! :smiley: We could set up a video call altogether, to clarify our objectives and see how we can help with your applications. Reading about your experiences here, it sounds like you would both be an amazing fit for any of our 3 projects related to BrainBox. So maybe you like the same project, maybe you like 2 different parts to focus on. Let’s find out :smiley: \ö//

What do you think about a call all together?
With respect to time zones, we were thinking during European morning could work. I am coordinating with the other 2 mentors and will write to you asap.

Thanks again for choosing our projects and being interested in working with us. :smiling_face_with_three_hearts:

katja, roberto & alexandra

1 Like

@katjaq

Thank you for writing back! It would be great to be part of a call together for further clarification. Looking forward to hearing from you about it :smiley:

@Alexandra_de_Sousa @katjaq
Greetings,
Myself Vishwas Singh, am currently a sophomore at IIIT-Allahabad, India, also I am a full stack web developer, my main areas of work include HTML/CSS/Js, ReactJs, NextJs, Django and Svelte. I have been actively contributing to open-source since Jan 2019, I would like to contribute to this project idea and the other two BrainBox projects, am looking forward to interact with the mentors so that I can also put my suggestions on the table :slight_smile:

1 Like

@katjaq
Thanks a lot and really excited to connect with all the mentors soon​:grinning_face_with_smiling_eyes::grinning_face_with_smiling_eyes:

1 Like

Hello again!

and hello to the discussion also @infern018 ! Sounds great!

Would you all be available for a video call all together next Monday, 15 March, after 11am GMT or Tuesday European morning (before 1pm GMT)? Let us know if you have any restrictions, please, so that we can find the date :slight_smile: (and also what would be the latest options for you on Monday, as we span several time zones :slight_smile:

\\ö// Looking forward to meeting you all! :smiley:

best
katja, roberto & alexandra

The above-mentioned time and date is perfectly fine for me,

looking forward to the meeting :smile: :smile:

1 Like

Monday, 15th March, after 11am GMT is good with me. In case that’s not a good time for @chetanya_tomar , then tuesday anytime between 9 am - 11am GMT is good with me. Hope this is okay. Looking forward to meeting everyone virtually! Thank you :smile:

@katjaq @Saarah_Asad
11 am Gmt time is totally good with me.
Looking forward to meeting everyone soon :smile: :smile:

1 Like

hello dear @chetanya_tomar @Saarah_Asad @infern018 !

Let’s meet on the BrainWeb https://brain-web.github.io/videoconference. See you in ~2 hours! :slight_smile:
Looking forward to meeting you :blush:

katja, alexandra, and roberto

2 Likes

Hopefully I’m not too late!

Hi there! I’m Nabil Tharwat. I’m a student currently enrolled in the Bachelor’s of Computer Science track at Cairo University, set to graduate in 2022. I’m a software engineer and have been building websites for over 3 years involving the use of frontend frameworks, backend technologies, and the NodeJS ecosystem in general. You can find some of my favourite projects here.

I’m interested in working on Brainbox, with this being my first contribution to the neuroscience community and ecosystem, and would love to take on this challenge to make access to these histological collections easier for researchers.

I have very rough ideas regarding the UI and how the filtering/querying operations would work, but I lack the knowledge in histology that would allow me to completely visualize how the data is analysed, annotated, and presented. Was that video conference recorded? If not, are there any resources that could help me reach better understanding of what this project involves?

Thanks!

CC: @katjaq @Alexandra_de_Sousa

Hi @KL13NT ! Thank you for reaching out! :smiley:

Ohh how unfortunate! We had a very nice meeting yesterday, but unfortunately did not record it. Sorry we missed you – we will try to catch you up otherwise. We are currently thinking about a little project task which will send along here in short.

We don’t really have any video material that could help here. To explore histological data for a visual impression, you can play around with some linked datasets for example: https://microdraw.pasteur.fr has 3 datasets linked to go and explore. You can select one of them (for example the BigBrain), click “Go” and view the data, zoom in to the neuron level, and draw some annotation.
We also took notes during our call: Framapad mensuel which I think can help you gain a good first idea :slight_smile:

On an other note, we have 2 other projects (related to histological data (MicroDraw) and brain imaging MRI data (BrainBox). We will meet tomorrow (Wednesday 1pm GMT on the BrainWeb, same link as above https://brain-web.github.io/videoconference ) to discuss these projects. We will very likely not dive into the details of the database, but we will probably present our tools again, where you will get to see the data involved :slight_smile: and how these tools work. If you have time, please feel welcome to join us. (but I really don’t know how relevant it would be for the database project itself rather than to see in which context the database would fit… :slight_smile: ).

Looking forward to hearing from you and maybe seeing you tomorrow (Wednesday, maybe your today by the time you read this :upside_down_face: )

very best
katja, roberto and alexandra

2 Likes

Hey @Alexandra_de_Sousa, I’ve got a few questions regarding the Metadata DB project.

  • Has this project been started yet? I couldn’t find a GitHub repo for it.
  • Will there be any online conferences regarding this?
  • If I have any more questions regarding this specific project, what is the best way to ask? Neurostars, email, or something else?
  • Will there be a channel for collaboration on this project?
1 Like

Hopefully this is not too late to join ?
I am Vamsi from IIT Palakkad, currently pursuing my 3rd year of study majoring in Computer Science And Engineering. I have a ton of experience in web development, especially using MEAN and MERN stack. I have experience in building full fledged websites from the build to hosting. I want to bring my expertise to contribute to this project. Can the mentors please help me out with the starting steps ?

1 Like

Hi @arnab1896 , where can I get the e-mail ID of @Alexandra_de_Sousa , I wanted to clear some doubts regarding the implementation of this idea…

1 Like

Hello! Let us know if you need help writing your project proposal (send us a google doc link). If there’s any questions, we’re happy to answer them here!

1 Like

MANAGED BY INCF