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Segmentation is an integral step of any bioimage analysis workflow, which involves delineating areas or objects of interest within an image 1 . All the measurements performed on the image, e.g. size, shape, counts, or pixel intensities are then assigned to these segmented areas or objects to...

Docker is discussed in the bioimage analysis world a lot these days. But what are dockers? How does Docker make life easier? In this blog post, I will try to explain the basics of docker and why it matters to biologists. Have you ever faced package dependency issues when creating Python environments...

Hi all, Due to issues with pip installation with CellProfiler on some platforms, we have released a version 4.2.6 with slightly updated dependency pins. If you are using the CellProfiler 4.2.5 application downloaded from our website, there is no need for you to update - 4.2.6 contains no changes to...

Microscopy in the cloud: CellProfiler and Cell Painting on Terra Authors: Carmen Diaz Verdugo, Stephen Fleming, Nicole Deflaux and Amy Unruh Carmen Diaz Verdugo is a Computational Scientist in the Precision Cardiology Lab, and a member of Patrick Ellinor’s group. Stephen Fleming is a Senior Machine...

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...

Beth Cimini In the Imaging Platform, we tend to work on a lot of big, complicated projects , with a lot of moving pieces and sometimes collaborators in many countries! This is fantastic for science, but when it comes to writing a paper, it can make just gathering all the information about "who did...

Fernanda Garcia-Fossa & Anne Carpenter In a typical quantitative microscopy experiment, biologists choose fluorescent biomarkers and measure particular features (that is “metrics”) that they hypothesize will be perturbed in their samples. But in image-based profiling, you aim to let the cells tell...

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...

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...

Melissa Gillis In the previous two sections of this blogpost I explained how I analyzed multiple methods to segment fluorescent images of collagen IV fibers, and generated accurate segmentation using an ilastik machine learning model. In this section I will explain how I constructed a CellProfiler...