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Browser-based Apps for Data Visualization

February 07, 2019

Minh Doan

Have you ever stumbled across some amazing data visualization tools that run entirely on a web browser (such as this and many others), and wished you could plug in your own data and...

Read More Browser-based Apps for Data Visualization

Annotating Images with CellProfiler and GIMP

June 07, 2018

Kyle Karhohs

Annotated image data is valuable for assessing the performance of an image processing pipeline and as training data for machine learning methods such as deep learning. When...

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Read More Annotating Images with CellProfiler and GIMP

The CellProfiler 2 User’s Guide to CellProfiler 3.0, Part II: Converting your pipelines

October 24, 2017

Beth Cimini

For those of you who’ve been with us for a long time though, the obvious next question after how to use the new test mode is will my old CellProfiler pipelines work in the new...

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Read More The CellProfiler 2 User’s Guide to CellProfiler 3.0, Part II: Converting your pipelines

The CellProfiler 2 User’s Guide to CellProfiler 3.0, Part I: Using the new Test Mode

October 24, 2017

Beth Cimini

Everyone here at the CellProfiler team is very excited about our new 3.0 release, and we certainly hope you are too!  CellProfiler 3.0 is much faster than any of our previous releases...

Read More The CellProfiler 2 User’s Guide to CellProfiler 3.0, Part I: Using the new Test Mode

Mo Data, Mo Problems: How to share big data with ease

August 15, 2017

Kyle Karhohs

# Sharing Image Data

At the Imaging Platform we frequently need to send and receive images between collaborators or forum users. Working with images can become challenging...

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Read More Mo Data, Mo Problems: How to share big data with ease

A Quantitative Path to Pathology

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...

Read More A Quantitative Path to Pathology

Quantifying microscopy images: top 10 tips for image acquisition

June 15, 2017

Anne Carpenter

Not every image you capture on your microscope is suited for quantification, no matter how nice they may look. Even though you might not notice any problems by eye, the tips outlined...

Read More Quantifying microscopy images: top 10 tips for image acquisition

It is plane to Z how FIJI is a great companion for visually verifying CellProfiler’s 3D segmentation

April 11, 2017

Kyle Karhohs

Now that CellProfiler can handle 3D images, how do you view the results? When processing 2D images, the IdentifyPrimaryObjects module will produce a figure that displays the original...

Read More It is plane to Z how FIJI is a great companion for visually verifying CellProfiler’s 3D segmentation

CellProfiler & Ilastik: Superpowered Segmentation

January 19, 2017

Kyle Karhohs

Joining forces


CellProfiler is capable of accurate and reliable segmentation of cells by utilizing a broad collection of classical image processing methods. Peruse the documentation on...

Read More CellProfiler & Ilastik: Superpowered Segmentation

Getting Started with CellProfiler in Batch

May 18, 2020

Guest Author

This post was written by a guest author, Jillian Rowe, who can be reached at jillian@dabbleofdevops.com. 

Running CellProfiler in batch mode is the ideal way to automate large...

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Read More Getting Started with CellProfiler in Batch

Help! I want to use CellProfiler Analyst but I ran my pipeline with ExportToSpreadsheet!

May 28, 2020

David R. Stirling

We’ve all done this before – CellProfiler Analyst needs a database file, but your CellProfiler pipeline that took days to run was set up to export spreadsheets. To make matters...

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Read More Help! I want to use CellProfiler Analyst but I ran my pipeline with ExportToSpreadsheet!

Getting started using CellProfiler from the command line

April 30, 2021

Beth Cimini

Cross posted from our GitHub wiki — check there for any future updates!

Running CellProfiler from the command line has a major advantage — you don't need to spend computational power or...

Read More Getting started using CellProfiler from the command line

Help! How does the Robust Background method work?

August 05, 2021

Pearl V. Ryder

 

The Robust Background algorithm is a powerful algorithm for automatically setting thresholds to segment objects of interest when your image contains mostly background. However...

Read More Help! How does the Robust Background method work?

Thinking like an image analyst, Part I: Project overview and data import

August 10, 2021

Pearl V. Ryder

One thing I’ve found very helpful in my journey as an image analyst is learning from others by observing their thought process when they tackle a new problem. In this series of five...

Read More Thinking like an image analyst, Part I: Project overview and data import

Thinking like an image analyst, Part II: Removing bright debris from analysis

August 17, 2021

Pearl V. Ryder

In the first post of this series, I gave an overview of this project and explained how I imported the data into CellProfiler. If you’d like to follow along in CellProfiler, the...

Read More Thinking like an image analyst, Part II: Removing bright debris from analysis

Thinking like an image analyst, Part III: Enhancing fibers for detection

September 01, 2021
 

Pearl V. Ryder

In the previous blog post in this series, I demonstrated how I masked out debris that was brighter than the fibers of interest. In this post, I’ll walk through how I enhanced the...

Read More Thinking like an image analyst, Part III: Enhancing fibers for detection

Thinking like an image analyst, Part IV: Detecting fibers as objects

November 05, 2021

Pearl V. Ryder

In the previous post in this “Thinking like an image analyst” series, I explained how I enhanced fibers to increase their brightness and applied a background subtraction to decrease...

Read More Thinking like an image analyst, Part IV: Detecting fibers as objects

Thinking like an image analyst, Part V: Making measurements and exporting the data for analysis

November 12, 2021

Pearl V. Ryder

In the previous posts in this series, I explained how I approached an image analysis project to segment extracellular fibrils, giving an overview of the project (Part I), showing how I...

Read More Thinking like an image analyst, Part V: Making measurements and exporting the data for analysis

Creating a Cloudwatch Dashboard to Monitor Distributed CellProfiler Runs

December 01, 2021

by Erin Weisbart


This explains how to set up a Dashboard in Amazon Web Services (AWS) Cloudwatch, which widgets we find most helpful for monitoring Distributed CellProfiler (DCP) runs in our...

Read More Creating a Cloudwatch Dashboard to Monitor Distributed CellProfiler Runs

Input Modules Tutorial

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...

Read More Input Modules Tutorial

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