Here we describe the open-source CellProfiler project, our effort to develop such a software system for the scientific community. CellProfiler simultaneously measures the size, shape, intensity and texture of a variety of cell types in a high throughput manner. Note that we focus in this paper not on the technical details of the software (which are described in the manual), nor computational validation of the mostly published algorithms, nor on a mechanistic study of any particular biological finding. Rather, we describe the system, validate the software for a variety of real-world biological problems, demonstrate the breadth of its utility (including on various cell types and assays), and hope to stimulate ideas within the biological community for future applications of the software.
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The following can be freely downloaded from the CellProfiler website [31]: CellProfiler for Windows, Mac, and Unix (compiled, not requiring MATLAB); CellProfiler's MATLAB source code; a full technical description of CellProfiler's algorithms and measurements in an extensive PDF formatted manual (Additional data file 1), identical to the information found in help buttons within CellProfiler; and pipelines to identify the various cell types in this paper (see Additional data file 2 for a list of the modules in each pipeline).
The technical description of these algorithms is omitted here but is available in the online help and manual, in addition to previously published references cited therein (Additional data file 1). The identification modules include a 'test mode' for comparing several algorithms side by side in order to choose the best approach. We have found that these cell identification methods are flexible to various cell morphologies. This flexibility is convenient but, more importantly, often allows accurate identification of cells with unusual morphologies within a population of normal cells.
Like most new software in the laboratory, the process of setting up a CellProfiler analysis may take several days if the user is learning the software for the first time. Several resources help at this stage: the built-in help, the manual (Additional data file 1), the online discussion forum [31], the 'test mode' for the Identify modules that show results from various options side by side, and built-in image and data tools to interact with processed images and cell measurements (Additional data file 5). The flexible, modular design and point-and-click interface make setting up an analysis feasible for non-programmers. Over time, experienced users typically require less than a day to set up an entirely new experiment (for example, a new cell type or unusual measurement scheme). When performing the same analysis on different image sets where sample preparation is the only variable, we test the analysis on a few sample images and sometimes change one or two settings in the Identify modules. This takes less than an hour and is essentially a quality control step. Once a pipeline is satisfactory, analysis can be performed on the local computer or automatically divided into smaller batches to be sent to a cluster of computers, described in more detail in later sections.
Cell count (used to probe cell proliferation/apoptosis/death) is a straightforward phenotype that has, nonetheless, proved challenging for many cell types due to the poor ability of existing software to separate clumped nuclei. For human cells (Figure 2a, left), CellProfiler's accuracy compared to manual counting is twice that reported for a commercial software package [25]. CellProfiler also counted the more difficult-to-identify Drosophila Kc167 cells (Figure 2a, right). Cell size was not previously measurable for many cell types, but CellProfiler's measurements were consistent with the gold standard, a Coulter particle size counter (Figure 2b). While an automated routine has been developed for this cell type [45], this is, to our knowledge, the first report on the quantitative accuracy of any software to count and measure cell size in Drosophila Kc167 cells and the results indicate that such screens are now feasible.
The following additional data are available with the online version of this paper. Additional data file 1 is the CellProfiler manual. Additional data file 2 shows the CellProfiler pipelines for experiments shown in this paper, listing the modules in the order used. Additional data file 3 is a table listing CellProfiler modules by category, with their descriptions. Additional data file 4 is a table listing the measurements made by CellProfiler modules. Additional data file 5 lists the data and image tools in CellProfiler, with their descriptions. Additional data file 6 is a figure showing an example from CellProfiler analysis of DNA content (cell cycle) in Drosophila Kc167 cells. Additional data file 7 is a figure showing histograms of shape and texture features for wild-type cells. Additional data file 8 is a table listing measures for the cytoplasm-nucleus translocation assay (Figure 4) for which the Z' factor is above 0.5.
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Inform is a programming language and design system for interactive fiction originally created in 1993 by Graham Nelson. Inform can generate programs designed for the Z-code or Glulx virtual machines. Versions 1 through 5 were released between 1993 and 1996. Around 1996, Nelson rewrote Inform from first principles to create version 6 (or Inform 6).[3] Over the following decade, version 6 became reasonably stable and a popular language for writing interactive fiction. In 2006, Nelson released Inform 7 (briefly known as Natural Inform), a completely new language based on principles of natural language and a new set of tools based around a book-publishing metaphor.
Andrew Plotkin created an unofficial version of Inform 6 that was also capable of generating files for Glulx, a virtual machine he had designed to overcome many of the limitations of the several-decades-old Z-machine. Starting with Inform 6.3, released February 29, 2004, Inform 6 has included official support for both virtual machines, based on Andrew Plotkin's work. Early release of Inform 7 did not support Glulx, but in August 2006 Glulx support was released.
On April 30, 2006, Graham Nelson announced the beta release of Inform 7 to the rec.arts.int-fiction newsgroup.[13] Inform 7 consists of three primary parts: The Inform 7 IDE with development tools specialized for testing interactive fiction, the Inform 7 compiler for the new language, and "The Standard Rules" which form the core library for Inform 7. Inform 7 also relies on the Inform library and Inform compiler from Inform 6. The compiler compiles the Inform 7 source code into Inform 6 source code, which is then compiled separately by Inform 6 to generate a Glulx or Z-code story file. Inform 7 also defaults to writing Blorb files, archives which include the Z-code together with optional "cover art" and metadata intended for indexing purposes. The full set of Inform 7 tools are currently available for Mac OS X, Microsoft Windows and Linux (since 2007).
On March 1, 2006, Short announced the release of three further games:[21]Bronze[22] (an example of a traditional puzzle-intensive game) and Damnatio Memoriae[23] (a follow-up to her award-winning Inform 6 game Savoir-Faire) were joined by Graham Nelson's The Reliques of Tolti-Aph[24] (2006). When the Inform 7 public beta was announced on April 30, 2006, six "worked examples" of medium to large scale works were made available along with their source code, including the three games previously released on March 1.[25][26][27]
Emily Short's Floatpoint was the first Inform 7 game to take first place in the Interactive Fiction Competition.[28]It also won 2006 XYZZY Awards for Best Setting and Best NPCs.[29] Rendition, by nespresso (2007), is a political art experiment in the form of a text adventure game. Its approach to tragedy has been discussed academically by both the Association for Computing Machinery[30] and Cambridge University.[31] 2ff7e9595c