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Johan Fredin Haslum

Person: Postdoctoral Fellow
I am a Postdoctoral Fellow at the Imaging Platform. I am interested in applying and developing machine learning methods for analyzing and representing the rich information captured in high throughput imaging datasets.

Lab Policy and Culture

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Photo credit: Juliana Sohn Our mission & ethos: Our mission is to uncover biological knowledge and new medicines by developing advanced methods to quantify and mine the rich information in images. Together, our team explores the inner workings of biological systems and makes discoveries that can...

Input Modules Tutorial

Blog: February 24, 2022
Barbara Diaz-Rohrer If you are working with single-channel images, you can just drag a few images into CellProfiler and start making your pipeline. Most of us, however, have images with multiple channels or more complex image metadata that you need to tell CellProfiler how to identify.The tutorial...

Cihan Ruan

Person: MLSC Intern
I am a researcher in artificial intelligence specializing in computer vision. I focus on applying cutting-edge AI models to practical problems, with an emphasis on cross-disciplinary applications and adapting state-of-the-art neural networks to new and emerging tasks.

Funding

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Since 2003, grants have been provided by... ​ ​ ​​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​

Announcing CellProfiler 3.1.8

Blog: December 21, 2018
Beth Cimini Happy holidays to everyone- we here at the CellProfiler team got you a little end-of-year treat in the form of CellProfiler 3.1.8. This is primarily a bugfix release, getting rid of some bugs in MeasureObjectIntensity, MeasureColocalization, ExportToSpreadsheet...

Announcing CellProfiler 3.1

Blog: July 26, 2018
Beth Cimini I’m excited to announce the release of CellProfiler 3.1. Our focus for CellProfiler 3.1 was polishing features and squashing bugs introduced in CellProfiler 3.0. We also started laying down the foundation for our next release, CellProfiler 4.0, that will transition CellProfiler from...

A Quantitative Path to Pathology

Blog: June 21, 2017
Guest Author This post was written by a guest author, Kun-Hsing Yu, who can be reached at Kun-Hsing_Yu@hms.harvard.edu. Lung cancer causes more than 1.4 million deaths per year. To diagnose lung cancer, pathologists prepare microscopic slides from surgical or biopsy samples, stain them with...

Customizing a Model for Fiber Segmentation, Part 2: Creating an ilastik Model

Blog: August 05, 2022
Melissa Gillis In the first part of this blogpost I described some of the tools I tried to accurately segment collagen IV fibers including, CellProfiler, Cellpose, and Piximi. Unfortunately none of these methods were successful in accurately segmenting the fibers so I decided to develop a machine...

How to export tiles of large histology images in QuPath

Blog: October 05, 2022
Rebecca Senft With slide scanners and other automated, high-throughput microscopes becoming more and more common, it’s important to understand how to work with the large image files they produce. Whole slide file formats (e.g., .mrxs, .svslide, .svs, .vms) are often massive when uncompressed (>40 GB...