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March 14^th 2022

EGAB Connecting the Mexican Bioimaging Community

National Laboratory for Advanced Microscope�Kick-off meeting

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What got you interested or started in imaging/microscopy?

I wanted to apply the mathemical theory learned during my bachelor’s degree to solve real life problems. Microscopy through image acquisition has allowed me to apply mathematical and computational knowledge to analyze images and extract relevant information.

Paúl Hernández

Instituto de Biotecnologia, UNAM

Adan Guerrero

Instituto de Biotecnologia, UNAM

Chris Wood

Instituto de Biotecnologia, UNAM

Team

About

Expanding Global Access to Bioimaging, 2022

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Brief Overview LNMA

Your Imaging Core

Technology and Expertise

Nanoscopy, single molecule characterization, image cytometry, molecular modelling, bioluminescent imaging, IA development in nanoscopy and spectroscopic microscopy.

Experience developing image analysis algorithms and supervised machine learning for segmentation and other functions

Confocal

Amnis

Nanoimager-s

Bioluminescence System

Time: ~2 mins

Use this slide to introduce your imaging core. For example, you could talk about the history of the core, imaging systems that you have or develop, previous outreach activities (have you trained or worked with users external to your organization?).

Who are your current users? How many users did your core have on average before and after the pandemic? Do you have external (outside your institution) or foreign users?

Technology and Expertise: What imaging systems and software does your core provide to biomedical researchers? Do you develop any new technology? Please also describe any teaching and outreach activities (teaching at regional workshops, increasing awareness of microscopy among middle and high school students, etc.)

Feel free to change the layout, formatting, and style, etc. You may add additional slides if necessary

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Project Description

Course on Artificial Intellence for image analysis

Project Goals

What do you plan to accomplish with this project?

Reach the community/core facilities to know about the different AI algorithms
Motivate the use of AI algorithms for image analysis in core facilities
Collaborate with the bioimage community to identify potential areas of AI application

Basics of machine learning algorithms

(Ilastik, Weka)

Basics of Convolutional Neuronal Networks

(U-Net)

Generate ground truth data (Annotation tools, FIJI, ImageAnnotator)

Training Convolutional Neuronal Networks

Apply the model to new data

Mode: Virtual

Date: To Be Determine

Session: 3 days

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Working Together

Is there an expertise or technology that you currently don’t have but that would help with your project?
* Access to annotated data to train supervised algorithms
* Similar projects to test the performance of the developed AI algorithms
What is the main challenge for your project that this community could help to solve?
* Sharing annotated data allows to reanalyze the data by other groups, generating new hypothesis, corroborating results and testing or developing new image analysis algorithms.
How can this community work together to help advancing bioimaging in your region?
* Creating a forum where people can post doubts about image analisis, adquisition and the own community can answer those questions, similar to image.sc