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Imagej cell counter plugin mac

Bug – Macro stops running when no object found 3D object Count

Since digital slide processing could be a time consuming task, the plugin allows the user to launch very long series of unsupervised tasks, which can be performed in free time overnight or week end. Folder and file parameters can be selected by browsing the file system. In the main dialog window, apart of input and output folders setting, a macro selection button allows the user to choose the file containing the macro to be executed on the tiles.

Most digital slide files are pyramidal, i. However, the order in which series appear into the file is not the same for all formats. Internal tile sizes are normally dependent on the system used for acquisition and are usually small x, or similar sizes. The plugin instead provides a parameter to set the size according to user needs. Typical sizes will depend on the algorithm that has to be applied and on the memory available. In addition to that, another parameter defines the overlap between tiles, identical for X and Y directions.

The last parameter defines whether the tiles are deleted or not after each processing step. Tiles are stored in TIFF format with a file name that reflects their position on the overall digital slide according to the following template:. Stored slides can then be reopened after their main processing step, since they are always identifiable if not automatically deleted.

This may enable multiresolution processing, backtracking algorithms, etc. The file name can be accessed also during processing, with techniques usual in ImageJ macro programming i. This allows to know at any time which tile is being processed, in which series and of which slide.


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However, since those data are often useful, in provided macro examples we defined a function that returns that data. The called macro should be designed to work on the opened image, and is responsible to close it and eventually any other window at the end of the execution. One potential limitation is that each run of the macro on a tile is independent. Thus, in principle is impossible to pass variables from one step to the other.

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However, ImageJ allows to save data in its Results table, which provides persistence among tile processing steps, as demonstrated in the example macros. In fact, we at first developed a rough algorithm for that, based on colour deconvolution [ 19 ], then we also adapted ImmunoRatio, an ImageJ plugin that has been validated for that [ 20 ]. However, we did not aim at a robust implementation for clinical use, but just as demonstration of usage and functionality. Thus, the implemented macros do not discriminate normal and stromal tissue, and in-situ components. In the macro examples we also implemented a set of functions to store variables or arrays.

They can be used as they are or as the basis for more complex storage schemas. File name and a short summary of macro content has been provided for each example macro. The ten digital slides for the test set ranged from Mpixel to 3. While not aimed at validation, the positivity calculated with the algorithm implemented in SlideJDemo2 achieved a Pearson correlation of 0. Fig 2 shows a sample slide.

Overall view of a sample slide and one high magnification detail. A macro with the same algorithm of SlideJDemo2 , but adapted to be applied to an entire slide, has been developed to check whether digital slides of the progesterone test set could be directly processed without SlideJ. In fact, it depends from the algorithm and from memory available to ImageJ, and thus we set our system for using a large amount of RAM for it 8GB.

However, 6 out of 10 slides—the largest ones- could not be processed directly due to out of memory errors, as expected. This even if the implemented algorithm is very simple. With our memory setting, the threshold for exhausting memory was put around Mpixels, with degrading processing speed in slides slightly below threshold, likely due to swapping. The SlideJdemo2 macro, called from CallerDemo2 , has been executed on the progesterone slide set, changing tile size in the following steps: , , , , , , , , Fig 3 shows throughput for each tile size. No out of memory errors have been recorded during execution of SlideJ.

Cell Counter plugin

Data is presented as box and whiskers plot minimum, 1 st quartile, median, 3 rd quartile, maximum. As it can be seen, smaller tile sizes result in slower processing, due to the overhead in accessing the original file and saving tiles. However, anything above pixels of tile size that is, 36Mpixels tiles is almost equivalent in terms of speed.

In the experiment setting, at pixels of tile size, the average time needed for processing one slide is 9. Whole slide images cannot always be directly opened and processed with ImageJ and similar software, due to the need of being fully loaded in main memory, which is not often practically possible. SlideJ provides a method to automatically process digital slides inside ImageJ. In principle, any digital slide format supported by Bio-formats now or in the future can be opened and processed using SlideJ. No specific workflow has been implemented, except the iterative loading of tiles from the digital slide.

Processing and analysis are left to a macro written in the ImageJ scripting language, which is applied to each tile. No other plugins implement this function at present. There are however some limitations. Persistence of partial results is implemented using Results Tables of ImageJ, which is a sort of workaround, although known to ImageJ users. Furthermore, at present we do not consider digital slides with more than one focal plane or time point. Finally, performance of macro-based processing is far from the needs of images as large as digital slides in production environments.

However, the intended use of SlideJ is mainly rapid prototyping and testing of processing algorithms on digital slides aimed at research, that could then be translated in Java code or other implementations.


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  • Browse Subject Areas? Click through the PLOS taxonomy to find articles in your field. Abstract The digital slide, or Whole Slide Image, is a digital image, acquired with specific scanners, that represents a complete tissue sample or cytological specimen at microscopic level. Introduction The digitalization of full glass slides containing tissue samples for microscopic analysis is a reality that is becoming stronger and opens to many opportunities [ 1 ].

    Material and methods Requirements In the process of designing the plugin, a number of requirements have been identified to assure the robustness of the plugin in a variety of usage scenarios. The requirements that have been identified are the following: The plugin should be usable with different digital slide formats. Using Bio-formats as input library already allows for this, but robustness over internal parameters of different formats, such as series position or tile size, has also to be guaranteed.

    Thus, the plugin should contain also configurable parameters. The macro to be executed should be stored in a file, which position is not fixed but passed as a parameter. Even if the macro is independent from the image being processed, the developer should be able to recognize the coordinates of the sub-image itself. Overlap between adjacent tiles should be configurable through a parameter. Tiles extracted from the digital slide can be automatically deleted after macro execution or left in a temporary folder, according to user preferences. The latter possibility allows for their availability even after their processing.

    It should be possible to invoke the plugin with its parameters, from another macro too, to further automate execution. Experimentation Three experiments have been made to demonstrate the effectiveness of SlideJ: To evaluate compatibility with common digital slide formats, we applied the plugin to all demo files hosted at the Openslide web site, which in turn are used to demonstrate Openslide features [ 18 ]. The last experiment has been carried out to evaluate performance of the system according to tile size.

    For this, 10 digital slides from breast cancer core biopsies, immunohistochemically stained for progesterone, have been randomly selected from a previously available set. They were acquired with an Aperio CS scanner, at 20x magnification and thus with a spatial resolution of 0. At first, an attempt to open and process the slides as they are has been made, to evaluate how many could be directly processed with ImageJ, in spite of their size.

    While we recognize that throughput heavily depends on the implemented algorithm, this experiment gives an idea to users on which tile sizes are better to address their implementations. Results Implementation The SlideJ plugin has been implemented in Java, using Bio-formats as input library and the fiji-lib. Download: PPT. Digital slide test set The ten digital slides for the test set ranged from Mpixel to 3. Performance The SlideJdemo2 macro, called from CallerDemo2 , has been executed on the progesterone slide set, changing tile size in the following steps: , , , , , , , , Conclusion Whole slide images cannot always be directly opened and processed with ImageJ and similar software, due to the need of being fully loaded in main memory, which is not often practically possible.

    References 1.

    1. Setup for Automatic Cell Counting

    Taylor CR. From microscopy to whole slide digital images: a century and a half of image analysis. Appl Immunohistochem Mol Morphol. Composite objects can encapsulate different color-coded marker structures in order to bundle features that belong together ObjectJ provides back-and-forth navigation between results and images. The results table supports statistics, sorting, color coding, qualifying and macro access.

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    A single file such as "MyProject. ObjectJ plugin have been developed to measure tree rings, eucalyptus leaves shape and cell count and measurments. Source: ObjectJ website.


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