Blog

Search results

28 results found

Best Practices for Jupyter Notebook

When you are new to the coding world, a lot of new information can be overwhelming. Staying organized might help ease the learning process. This blog post is about simple ways to organize your Jupyter notebooks to make them more reproducible and user-friendly. First, let me begin by introducing the...

How to export tiles of large histology images in QuPath

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...

Customizing a Model for Fiber Segmentation, Part 4: Analyzing the Results

Melissa Gillis In the final section of this blogpost series, I will discuss some of the benefits and drawbacks of this model and discuss some of the data I acquired from the images. This model was able to successfully segment the images that were not able to be accurately segmented by Pearl’s...

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

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...

UnmixColors Modules Tutorial

Mario Costa Cruz If you have color images stained with light-absorbing dyes, the UnmixColors module might be able to separate the dyes into separate channels so that they can be analyzed separately. Separating the dyes into channels can be a difficult task with traditional methods such as split...

How to Normalize Cell Painting Data

Rebecca Senft Let’s talk about normalization: why we normalize data and how we choose a method for normalizing data in Cell Painting experiments. We’ll consider a theoretical example experiment including two plates, each with a different cell type (neurons and fibroblasts). Plates include similar...

Input Modules Tutorial

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...

Creating a Cloudwatch Dashboard to Monitor Distributed CellProfiler Runs

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 Cloudwatch Dashboard, and what you might learn from each widget. AWS Cloudwatch Dashboards are “customizable...