The plugin will prompt you for an output directory to store the stabilized image sequence. To alleviate the slower speeds, select “ignore Z position” within the second GUI.To process very large image stacks, import the stack with the “Use Virtual Stack” option enabled. If the computed image does NOT show up as one large square with a patchwork of squares, your data set has varying z-values. To check if this could be a problem with your dataset, use the menu title to access Plugins › Stitching › Visualize Tiles. This will cause the stitching program to include tiles of black space wherever a tile has a z coordinate less than the maximum z coordinate within the file. Check the amount of installed RAM on your computer to ensure you do not try to allocate more memory than exists.Īnother speed reduction will occur if the tiles used have varying z coordinates.Enter the amount of memory you would like to be allocated to the Fiji application in megabytes.Open Memory from the menu item Edit › Options › Memory & Threads.If “use virtual memory” has been selected but the stitching plugin is still taking a considerable amount of time, try allocating more memory to the process. This will invert the selected coordinates before stitching the image create the correct image. Depending on which axis the image has been inverted upon(the user will need to know this) select the corresponding option within the second dialog box. After stitching, if the output image appears incorrect, redo the stitch. The plugin is unable to discern the inversion without human intervention. Troubleshooting with the Grid/Collection Stitching plugin Inversion of CoordinatesĬertain data sets have caused an inversion of coordinates when stitched together. Click ok and the images will begin to be stitched together.Alternatively, more memory can be allocated to the Fiji operation.If the data computed is too large for computer memory, check “use virtual memory.” This will be considerably slower, but will save RAM.Reduce “Increase overlap” to 0 and uncheck subpixel accuracy.if Prairie or WiscScan are used, uncheck “compute overlap.” Both softwares calculate fairly accurate coordinates beforehand.To learn about other fusion methods, please visit the Stitching page.To save time, only use linear blending for presentation pieces. Without it, tile lines will be clearly seen if the image is to be blown up.
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