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Continuing on the 1001x1002x1003 example, assume it had “xyz” as axis order. To change the slicing axis, use the “Transpose to Axis Order” control to bring the axis you need to the front. This information is displayed in the dialogue if you select a “sequence” output format. For example, if your dataset is 1001x1002x1003 pixels and you choose to export it as an image sequence, it will export 1001 images, 1002x1003 pixels each.
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For some formats, this doesn’t matter so much (e.g. Transpose to Axis Order: This setting sets “outermost” and “innermost” axes (and so on).For example, prediction data is typically given a range of, but you can scale it to the range of for easy viewing with other software. Renormalize from: Use this setting to scale the range of your results.Use this setting to save your results with an alternative pixel type. Convert to Data Type: If unchecked, the results will be exported with whatever pixel type is shown in the “Source Image Description” fields.Transformations: These controls provide fine-grained control over the output result format.to export the first 100 z-slices in a dataset, set the z range to [0, 100). Note: The ‘stop’ field is non-inclusive! e.g. Each dimension of the region’s bounding box can be edited with separate start, stop controls. It may happen that parts of the dataset outside the crop you selected are presented in the blocks). Results outside of the specified region will not be exported, and may not be computed during the export process (ilastik internally computes the results blockwise. Cutout Subregion: This can be used to select a specific region-of-interest to export.
Caj viewer file cannot be viewed normally full#
Source Image Description: This is a description (shape, data type, and axis order) of the full image volume you can export with this interface.The Export button generates individual output files corresponding to the selected dataset. To change the location, open the export settings dialog by clicking the Choose Settings button on the left. Besides, you can see the location of the output file, where the results for this dataset will be exported. The nickname is usually the name of the input file or, for stacks, a combination of the names of the files in the stack. On the right you can see all your datasets listed by their nickname, as defined in the data selection applet. Here you can control all the necessary parameters to export what you need, where you need.Įxport All: runs the export for all input files based on the settings, including output file names and locations, specified in the export settings dialog. For example, in pixel classification you can export label probabilities or segmentations.Ĭhoose Settings: opens the export settings dialog explained below. Source: offers a drop-down menu of layers which can be exported. The following controls are available in the panel: The GUI can be used to change export settings as well as to bulk export all of the data. In pixel classification, for example, the applet is called “Prediction Export”.
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The export step is handled through the data export applet in ilastik.