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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 fibers in order to increase their brightness and decreased the background intensity of the images. If you...

Melissa Gillis Segmenting fibers using traditional cell segmentation software can be challenging. Because most biological cell segmentation tools were designed for cells, most programs have difficulty identifying and distinguishing longer and thinner objects such as fibers. Also, unlike cells...

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...

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...

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, since it contains the largest number of tunable parameters of any thresholding algorithm in CellProfiler, it...

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 memory creating the graphical user interface (GUI) that you're used to using in CellProfiler! It also...

Anne Carpenter Clearly communicating the impact of your research is one of the most important skills you need to develop as a scientist, and yet typically it is only taught by doing (and if you are lucky, feedback – especially critical feedback). Clear communication is important to get funding and...

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 simply due to their file size. Memory and disk limitations are often irritants when analyzing images, but in some...