Blog

David R. Stirling We have now released CellProfiler version 4.0! Download it here. The primary goal of this release has been to migrate CellProfiler from Python 2 to Python 3. This has involved extensive restructuring of the code base, leading to a lot of “under-the-hood” improvements. Important...

David R. Stirling We’ve all done this before – CellProfiler Analyst needs a database file, but your CellProfiler pipeline that took days to run was set up to export spreadsheets. To make matters worse, you also need a .properties file explaining what to do with that database. Fortunately, you don’t...

Guest Author This post was written by a guest author, Jillian Rowe, who can be reached at jillian@dabbleofdevops.com. Running CellProfiler in batch mode is the ideal way to automate large scale analyses. Or not so large scale analyses that you prefer to automate! One of the benefits of running...

Beth Cimini One of the most common questions I’m asked when helping a collaborator with an image analysis project is: “How do I know when my analysis workflow is doing well enough at finding the objects or measuring the things I care about?” Unfortunately, it’s also one of the hardest questions to...

Kyle Karhohs Imaging tissue slices provides a wealth of data about the spatial composition and number of the various cell types that make up a tissue. Interactions among cells within a tissue are crucial to understanding the role of the inflammation that is triggered by the invasion of cancerous...

Beth Cimini Hello all! It’s been a crazy last few months for the CellProfiler team, as we’ve been hiring some new members to the team and working hard on the transition to Python 3, which will bump us into CellProfiler version 4. Keep your eyes peeled for exciting content in the future! We did want...

Minh Doan Have you ever stumbled across some amazing data visualization tools that run entirely on a web browser (such as this and many others), and wished you could plug in your own data and visualize it? Or, as a biologist, you may know of a good analytic tool, but it either costs too much...

Beth Cimini Happy holidays to everyone- we here at the CellProfiler team got you a little end-of-year treat in the form of CellProfiler 3.1.8. This is primarily a bugfix release, getting rid of some bugs in MeasureObjectIntensity, MeasureColocalization, ExportToSpreadsheet...

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...

Jeanelle Ackerman You’ve earned degrees, authored papers, mentored supervisees, and traveled far and wide to speak about your work… And ideally it’s nicely showcased in your resume or curriculum vitae (CV), all updated and ready to go. But, if you’re like most academics, your CV is a sorely outdated...