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    When To Say ‘Good Enough’

    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 answer!  In an ideal world, we’d be able to achieve perfect recognition and/or segmentation of our biological objects every time, and get out perfect data! Alas, biology is almost never so...

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    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...

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    ScienceSnippets: Building communication skills and sharing what you love

    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 resources for your work, to publish it, to entice collaborators, to impress colleagues and supervisors, … and to not be boring at parties when asked “So what do you do?”

    With the help of the Broad Communications lab, I put together an...

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    Tricks for maintaining your CV/resume with Google Docs: easy to edit, immediately published

    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 But, if you’re like most academics, your CV is a sorely outdated PDF and upon its request, you always find yourself scrambling to dig up recent accomplishments to prove you’ve not just been lounging around for the last 6 months (or years). And updating it requires locating an elusive latest version of a Word...

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    Tracking projects with Gmail tags: Collaborating through email

    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, let me describe the problem we are trying to solve: we need a way/place to post project updates, raw data, and emails about a given project, so everyone in the lab can have access to info (most...

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    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...

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    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...

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    Z-score big! A game plan for image-based profiling

    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 you wanted to give this approach a try, but been overwhelmed by the computational options available?

    Our recent paper, ...

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    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...

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    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.

    ...

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    Screening a million compounds for the price of a few thousand?

    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 materials such as human primary cells that are in short supply.

    Might there be a shortcut allowing you to screen a huge chemical library without the expense? If you have image-based screens of a large compound set on hand, this ...

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    Help! Why do my output images seem all black?

    Beth Cimini

    Double clicking on the output images produced by CellProfiler sometimes opens up a screen in your operating system’s default image viewer that looks all black. This can make it seem like your pipeline didn’t work or didn’t produce the right output. However, this can happen for a couple of reasons:

    (a) If you’re exporting objects and have only a few objects in your image
    (b) If you’re exporting 16-bit images

    This has to do with the fact that most non-scientific photo software is designed to show 256 levels...

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    Be a histology hero with CellProfiler

    Minh Doan

    Thanks to the rapid advancement in image processing, we now have so many techniques to characterize cellular and subcellular objects (hooray CellProfiler!) Measuring cultured cells in monolayers is (usually) easy…but what about examining how cells interact with each other and their surroundings? Such experiments are often conducted using highly confluent cell cultures, tissue sections, or densely cell-packed organoids. At this level, clusters of cells gather, tightly bind and overlap to form cell niches, and often in a single area...

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    Help! Why does CellProfiler say it can’t find any valid image sets?

    Beth Cimini

    Defining the input to CellProfiler can be the hardest part of getting your pipeline set up and your analysis underway.  Incoming images are configured in the first 4 modules of CellProfiler – Images, Metadata, NamesAndTypes, and Groups – which offer lots of flexibility. But it’s sometimes confusing what each one does, and it’s not always obvious which ones you need for your experiment.

    If you have mistakes in any of these modules, you may run across the dreaded errors ‘The pipeline did not identify any...

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    Looking for the Unexpected: Unbiased Image Analysis

    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 in mind phenotypes to measure, so you use CellProfiler to accurately The
    ...

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    Welcome to the CellProfiler Blog!

    CellProfiler Team

    The CellProfiler team is excited to announce the launch of our new blog!

    Articles will have a variety of topics, ranging from general knowledge, to specific module use and relevant literature spotlights. At the CellProfiler Forum, we answer all kinds of questions straight from the community; here at the blog we proactively post content that we think will be new and interesting to you. We encourage you to comment and start discussions on our posts – the blog is integrated with our forum so that the conversation...

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    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!

    A CellProfiler Approach to Analyzing Tissue Data

    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 cells. The strength of the inflammatory response has been linked to the prognosis of certain cancers such as lymphoma.

    Quantifying the spatial relationship among cells in the crowded environment of a tissue requires reliable segmentation...

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