Blog

Authors: Beth Cimini, John Kitchin, Andrew Rosen, and Anne Carpenter What is the COA form? NSF requires you to report all “Co-authors on any book, article, report, abstract or paper with collaboration in the last 48 months” in Table 4 of the COA form, for certain people (e.g. PI, Co-PI, Senior/Key...

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...

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...

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...

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 Science...

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...

Anne Carpenter Biologists are coming up with more and more complex physiologically-relevant assay systems and scaling them up for screens. From co-cultured cells to C. elegans to 3D organoids and tumor spheroids, these assay systems can be challenging, expensive, lower-throughput, and/or rely on...

Anne Carpenter So you already know how to put together an image analysis pipeline to measure particular phenotypes of interest? Great! Have you ever considered looking for the unexpected? Say you are comparing two treatment conditions, such as a negative control vs. a hormone treatment. You may have...