12/24/2023 0 Comments Czi file imagej![]() > It expects multiple channels and tries to open them thus I need to set the range. Problem: It does not open the selected file as individual file. > This pattern is repeated within each following time point. > Index 4 (first file of new timepoint): no channels recognized. > Index 3: C Begin = 1 C End = 4 620 planes (4C x 155Z) > Index 2: C Begin = 1 C End = 2 310 planes (2C x 155Z) > The next file with index 1: C Begin = 1 C End = 2 310 planes (2C x 155Z) > Interestingly if I give this file an index (such as 0) the behaviour is different then it does not recoginze any channels. > For the first file of the dataset without index: C Begin = 1 C End = 4 620 planes (4C x 155Z) > The range for the z slices are correct. > This opens the Bio-formats Range option. > Hyperstack Open Files Individually Color mode: Default Autoscale Specify range for each series. > For opening these files by dragging them into Fiji or selecting them via Bio-Formats Importer I use the following settings: > Time point 2 Channel 1 Right Illumination > index 4 > Time point 1 Channel 2 Left Illumination > index 3 > Time point 1 Channel 1 Left Illumination > index 2 > Time point 1 Channel 2 Right Illumination > index 1 > Time point 1 Channel 1 Right Illumination > no index > Thus there are 4 files per time point with the follwing order when they are saved by the microscope: Each dimension is saved as an individual. > The 2 illumination sides are not fused. czi dataset which is a 2 channel 2 illumination side single view timeseries. On, at 15:11, Christopher Schmied wrote: Run("Bio-Formats Importer", "open="+file+" color_mode=Default display_metadata display_ome-xml specify_range view=Hyperstack stack_order=XYCZT series_2 c_begin_2=1 c_end_2=1 c_step_2=1 z_begin_2=1 z_end_2=1 z_step_2=1") Run("Bio-Formats Importer", "open="+file+" color_mode=Default display_metadata display_ome-xml specify_range view=Hyperstack stack_order=XYCZT series_1 c_begin_1=1 c_end_1=1 c_step_1=1 z_begin_1=1 z_end_1=1 z_step_1=1") The other way is to use ImageJ macro, where you can also specify a subset of data to open, e.g.: You’ll be prompted with Import options, in the “Memory management” select “Specify range for each series”, which will give you an option to specify a subset of data. From the GUI using Plugins (menu)->Bio-Formats->Bio-Formats Importer choose. There are two ways to open a stack, time point or series without reading the whole. They will open but as you've noticed the metadata may be wrong. The indexed files may not give you the expected result. CZI is to always point the Bio-formatas importer at the master file (the one with no index). Indexed = true (false color, 16-bit LUT: 3 x 65536) I have checked the files and everything looks fine. Next message: Making permanent and public links in omero?.Previous message: Bio-Formats Importer.Hence, I would recommend you to use the Image Calculator (category: Community Contributions > KNIME Image Processing > Image > Process, or just search) of the stable Image Processing Extension for now and we'll fix the ImageJ2-Integration-issue.Bio-Formats Importer. You were appearently using the Image Calculator.-node of the imagej2 intregration which still is quite experimental (so is ImageJ2 itself). Execute failed: Required service is missing: : in the Image Reader context menu or the Table Cell View node) or put the Image Normalizer- or Image Converter (with the Normalize and Scale-Option) after you read the images.Ģ. So, you can either view the images by opening the Table Cell View (e.g. if its an UnsignedShortType image, pixel values can range from 0 to 655535, but probably the pixels in your image only take values way below that maximum value). the pixel values do not cover the whole range of the pixel domain (e.g. The images you read are probably not normalized, i.e. the problem that the output port only shows black images:
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