Blog

Anne Carpenter As the PI of the Carpenter lab (a.k.a. Broad Institute Imaging Platform, including the CellProfiler team), people often ask how I manage so many ongoing collaborations: we discuss 50+ external projects each year so it is a lot to track! I am happy to reveal our secrets. The goal First...

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 assessing the performance of a CellProfiler pipeline, for example a pipeline that segments nuclei, the annotated...

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, and the addition of volumetric processing is a huge game changer. CellProfiler 3.0 looks pretty similar...

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 version? We feel the same way – the pipelines you’ve accumulated over the years are precious resources! The good...

Anne Carpenter We are thrilled to announce that CellProfiler 3.0 is now released! Download it here . Eighteen months in the making, this is the first version of CellProfiler that can identify objects in 3D images volumetrically – the result of a collaboration with the Allen Institute for Cell...

Juan Caicedo As described in our lab’s recent review article , there are so many great reasons to use microscopy images to create signatures of perturbations: identifying phenotypes associated with disease, identifying chemical mechanisms of action, and discovering gene functions, among others. Have...

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...

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...

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 here for acquiring and storing images can improve the quality of data derived from digital image...

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 image next to the segmented image to make validation fast and convenient, a side-by-side comparison...