Blog

    Browser-based Apps for Data Visualization

    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, requires programming expertise, or requires bundled installations of many other dependencies that might not be compatible...

    Read more about Browser-based Apps for Data Visualization

    The CellProfiler 2 User’s Guide to CellProfiler 3.0, Part I: Using the new Test Mode

    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 to what you’re used to, albeit a bit sleeker than previous versions. While most of it still behaves exactly how you’re used...

    Read more about The CellProfiler 2 User’s Guide to CellProfiler 3.0, Part I: Using the new Test Mode

    The CellProfiler 2 User’s Guide to CellProfiler 3.0, Part II: Converting your pipelines

    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 and bad news is that the answer is Yes, mostly. In order to facilitate the...

    Read more about The CellProfiler 2 User’s Guide to CellProfiler 3.0, Part II: Converting your pipelines

    A Quantitative Path to Pathology

    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 appropriate chemicals, and observe the visual patterns of cell morphology under the microscope. This manual (and often laborious) approach is the gold standard for lung cancer diagnosis and...

    Read more about A Quantitative Path to Pathology

    Quantifying microscopy images: top 10 tips for image acquisition

    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 analysis. These tips are a bit CellProfiler-centric but generally applicable to any quantification you might do.

    ...

    Read more about Quantifying microscopy images: top 10 tips for image acquisition

    Help! I want to use CellProfiler Analyst but I ran my pipeline with ExportToSpreadsheet!

    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 need to re-run the entire experiment to get your data into CellProfiler Analyst. This blog post will cover how to convert a spreadsheet into a database and make a usable .properties file with which to load it into CellProfiler Analyst.

    ... Read more about Help! I want to use CellProfiler Analyst but I ran my pipeline with ExportToSpreadsheet!

    Mo Data, Mo Problems: How to share big data with ease

    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 cases, such as multi-dimensional images and whole-slide scans, images’ file sizes can be large enough that even accessing images becomes a major roadblock, especially when the size starts to rival the size of desktop or laptop hard...

    Read more about Mo Data, Mo Problems: How to share big data with ease

    It is plane to Z how FIJI is a great companion for visually verifying CellProfiler’s 3D segmentation

    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. However, the extra dimension in 3D complicates this approach, because the 3D image must be transformed in some manner in order to appear on a flat surface (e.g. the monitor or phone you’re using to read this blog post!). This blog post...

    Read more about It is plane to Z how FIJI is a great companion for visually verifying CellProfiler’s 3D segmentation

    CellProfiler & Ilastik: Superpowered Segmentation

    Kyle Karhohs

    Joining forces


    CellProfiler is capable of accurate and reliable segmentation of cells by utilizing a broad collection of classical image processing methods. Peruse the documentation on the IdentifyPrimaryObjects module, for example, to get a sense of these, e.g., thresholding, declumping, and watershed. However, despite the many problems CellProfiler can readily solve, certain types of images are...

    Read more about CellProfiler & Ilastik: Superpowered Segmentation