iiinova — where your digital self keeps evolving

Reposted by Esteban Miglietta

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 26/06/2026

Levin, aided by local DL expert @gnodar.bsky.social, designed several variational autoencoders (VAEs), incorporating the transcripts, nuclear image, cell membrane image, or some combo. Figuring out the joint representations took some doing, but eventually we got some models that worked nicely (4/x)

A diagram of a variational autoencoder, with input images on the left, a latent space in the middle, and reconstructed images on the right. 5 different sets of input images are shown, labeled VAE 1-5.

121

Reposted by Esteban Miglietta

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 26/06/2026

Because we're us, we were excited about image-based ST and including information from the images themselves, which spun the project into a new direction - what information could we add to spatial transcriptomics by the images themselves? (3/x)

111

Reposted by Esteban Miglietta

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 26/06/2026

This project was initially conceived in computer-science-land by the fantastic co-first author Levin Moser, and then brought to biology-land by the fantastic co-first author Kamal Hamid. Levin had worked on Piximi, and wanted to work on graph neural networks for spatial transcriptomics (ST). (2/x)

121

Reposted by Esteban Miglietta

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 26/06/2026

A week-overdue 🧵on the newest paper from the Cimini lab- do you ever do spatial transcriptomics? If you do, and you want free extra phenotypic info, step in to learn more about "Evaluating integrative strategies for incorporating phenotypic features in spatial transcriptomics". 🧪 (1/x)

onlinelibrary.wiley.com

Evaluating integrative strategies for incorporating phenotypic features in spatial transcriptomics

Spatial transcriptomics (ST) encompass technologies that measure gene expression in tissue samples without disrupting their organisation, unlike other single-cell techniques. In imaging-based ST spec...

195

Esteban Miglietta @emiglietta.bsky.social · 07/05/2026

If you like microscopy and image analysis and would love to have a real positive impact on the community, don't miss on this chance! You would be working with some of the most talented and ridiculously kind people you can find! (Also happy to chat about my experience there with anyone interested!)

010

Reposted by Esteban Miglietta

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 14/10/2025

Big news! Our week-long #bioimageanalysis bootcamp is BACK! Learn how to think about bioimage analysis like the pros do, learn what corrections you should (and shouldn't!) apply to your images, learn open source tools, and more. Apply NOW at broad.io/BAB3 for our January 2026 course!

A flyer for the Bioimage Analysis Beginnings Bootcamp - blue and white with a picture of cells on the top. It says "Learn core bioimage analysis skills using open-source tools for light microscopy. Open to participants at all skill levels." It also says it will be held a the Broad Institute, 415 Main Street, Cambridge MA USA, on Monday to Friday January 12th-16, 2026, from 9-5pm. Registration is $750 academic, $1250 industry, and applications are open at broad.io/BAB3

04227

Esteban Miglietta @emiglietta.bsky.social · 04/09/2025

🔬Are you interested in applying colocalization analysis to your microscopy image data? 💡Check out my new video on colocalization metrics on the Center for Open BioImage Analysis (COBA) youtube channel! www.youtube.com/watch?v=Ktx9...

youtube.com

Exploring and Understanding Colocalization Metrics

YouTube video by COBA: Center for Open Bioimage Analysis

171

Reposted by Esteban Miglietta

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 29/08/2025

Need AI-ready image data? Delighted to say that the Cell Painting Gallery (labor of love from two of the best colleagues around, @erinweisbart.bsky.social and @shantanu-singh.cc ) is now officially one of 10 featured datasets for NSF's National AI Research Resource Pilot. Congrats folks! (1/2)

nsf.gov

NSF expanding national AI infrastructure with new data systems and resources

The U.S. National Science Foundation today announced two major advancements in America's AI infrastructure: the launch of the Integrated Data Systems and Services (NSF IDSS) program to build out...

1152

Reposted by Esteban Miglietta

Damian Dalle Nogare @damiandn.bsky.social · 05/08/2025

Small brushes Small brushes *Bangs table* SMALL BRUSHES

031

Reposted by Esteban Miglietta

Michael Clemens @mclem.org · 27/05/2025

The US Administration has indefinitely blocked *all* student visa applicants from getting a visa interview. Worldwide, unconditional, no end date. All. International students are crucial to the US university system, American innovation, and future US prosperity.

forbes.com

Rubio Reportedly Pauses New International Student Visa Interviews

More than 1.1 million international students were enrolled at U.S. colleges and universities in the 2023-2024 school year.

2897526

Reposted by Esteban Miglietta

The Company of Biologists @biologists.bsky.social · 27/05/2025

We are featuring Mariana De Niz, co-organiser of our 2025 Global South Workshop, former @prelights.bsky.social author and @focalplane.bsky.social correspondent, as an extraordinary biologist this week. #100biologists @marianadeniz.bsky.social

163

Reposted by Esteban Miglietta

will-j-moore.bsky.social @will-j-moore.bsky.social · 23/05/2025

More examples of @zarr.dev OME-Zarr data being used for cool stuff!

092

Reposted by Esteban Miglietta

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 01/05/2025

BIG NEWS - for the first time ever, we're running a Bioimage Analysis Beginnings Bootcamp. Learn #bioimageanalysis from awesome folks, and gain familiarity with some new tools as well as how to pick the right tool in the first place. Aug 4th-8th - apply here (soon!) forms.gle/d2fCXsrWHVP8...

Ad for the Bioimage Analysis Beginnings Bootcamp at the Broad Institute.

Where & When
Broad Institute, 415 Main Street, Cambridge MA (in-person only)
Monday–Friday, August 4–8, 20259:00 AM – 5:00 PM

About the Bootcamp
Learn core bioimage analysis skills using open-source tools for light
microscopy in this hands-on, in-person course. The Bootcamp
covers annotation, segmentation, and deep learning fundamentals.

Fee: $600 (Academic/Non-Profit) | $1000 (Industry/For-Profit)
For more information email ImagingAdmin@broadinstitute.org

06441

Esteban Miglietta @emiglietta.bsky.social · 29/04/2025

If you need help with you image analysis, this is your chance to get free advice from experts!

010

Reposted by Esteban Miglietta

Rita Strack @ritastrack.bsky.social · 10/04/2025

Your yearly reminder to acknowledge the core facilities you use and their staff scientists in your papers. These scientists are a crucial part of the scientific ecosystem and to continue to exist they need tangible credit for their work. Plus their associated expertise adds credibility to your work.

7485165

Esteban Miglietta @emiglietta.bsky.social · 10/04/2025

🚨Serie de Talleres para Latinoamérica🚨 Con el equipo de @bethcimini.bsky.social en el @broadinstitute.org, y COBA organizamos una serie de Talleres gratuitos en línea sobre análisis de imágenes para Latinoamérica … en ESPAÑOL y PORTUGUÉS!!🎉🎊 broad.io/latam_worksh... Fecha límite: 23/4/2025

0109

Esteban Miglietta @emiglietta.bsky.social · 10/04/2025

🚨Latin American Workshop Series🚨 The team from @bethcimini.bsky.social‘s lab at @broadinstitute.org and the Center for Open Bioimage Analysis will host three free online image analysis workshops for LATAM ... in SPANISH🇪🇸 and PORTUGUESE🇧🇷!!!🎉🎊 broad.io/latam_worksh... Deadline: April 23rd, 2025

02317

Reposted by Esteban Miglietta

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 08/04/2025

Bioimaging and bioimage analysis friends, some help if you have 2-3 mins; for a paper, we're trying to estimate the number of biologists trained in open source software or tools in the last ~5 years. (1/2) #bioimaging #microscopy #bioimageanalysis

12834

Reposted by Esteban Miglietta

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 07/03/2025

We're once again hiring a summer (+?) #bioimage #bioimageanalysis #software intern! Due to requirements of the funding program, you must be a current student, as well as work onsite in MA (+ have US work permission). Details at the link below. Spend your summer making great tools with fun people!

forum.image.sc

Software engineering intern - summer/fall 2025 - Cambridge, MA USA

If you are a current student (undergraduate/masters/PhD) with permission to work in the US and ability to work in-person in Cambridge, MA, US, consider a summer internship in the Broad Institute Imagi...

02218

Reposted by Esteban Miglietta

GloBIAS @globias.bsky.social · 13/01/2025

Call 4 Help Pilot Event by GloBIAS, 22 Jan–5 Feb 2025! Offering life scientists a chance for hands-on guidance & support for #bioimage_analysis using Napari, Ilastik & CellProfiler. 💡 Details: www.globias.org/activities/c... 🔗 Sign up! Application until Friday 17 Jan: forms.gle/7hsJgramrFXB...

forms.gle

02522

Reposted by Esteban Miglietta

Sarah McAnulty, Ph.D. @sarahmackattack.bsky.social · 30/12/2024

Would appreciate a RT from the scientists for this one! We have 665 scientists in the spring database and I want to get us to about 1000 before we set the teachers loose on the database for January matches.

4190214