http://nanosims.geo.uu.nl/nanosims-wiki/ 2026-05-28T09:32:28+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/ http://nanosims.geo.uu.nl/nanosims-wiki/lib/tpl/dokuwiki/images/favicon.ico text/html 2017-11-16T08:36:26+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:additional_output_options?rev=1510817786&do=diff Additional output options 2017-11-04: A number of extra options for tweaking the appearance of the output have been added. Back to the list text/html 2017-11-16T04:59:11+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:annotated_scatter_plots?rev=1510804751&do=diff Annotated scatter plots 2014-11-27: When processing multiple NanoSIMS datasets, I end up with a scatter plot of ratios in many different ROIs for a number of different treatments. I want to be able to interact with this scatter plot, for example, to find out the identity of an apparent outlier. text/html 2017-11-16T06:55:31+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:auto_process_datasets?rev=1510811731&do=diff Auto-processing multiple datasets 2016-02-15: I have analyzed 10 nanosims datasets. For each dataset I accumulated the planes (sometimes with, sometimes without the drift-correction applied), defined and classified ROIs, exported images and data in ROIs for 13C/12C and 12C15N/12C14N ratios. However, now I realize that I also need to calculate and analyze the 31P/32S ratios as well as the cell sizes. Can I do this without re-processing each file separately? text/html 2017-11-16T08:38:55+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:depth_profiles_multiple_datasets?rev=1510817935&do=diff Depth profiles in ROIs from multiple datasets 2017-11-04: I have analyzed 10 datasets. In each dataset I defined ROIs, classified them, and calculated 13C/12C and 12C15/12C15N ratios in each ROI. Now I realize that I also need to check depth profiles of these ratios in each ROI to quantify their vertical variability within the sample. I could do it by reprocessing each dataset again, but is there be a more efficient way? text/html 2017-11-16T04:41:24+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:display_xyz_stacks?rev=1510803684&do=diff Display XYZ stacks 2014-11-21: Nanosims data acquired in the image mode form a 3-dimensional data-cube, where the detected ion counts vary as a function of the lateral (X and Y) and vertical (Z) co-ordinates. I want to be able to display this variation. text/html 2017-11-19T10:17:23+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:hue_intensity_correction?rev=1511083043&do=diff Suppressing the noise in ratio images due to low ion counts 2017-11-04: The images of my ion counts (e.g., 12C14N and 12C15N) look beautiful, but when I make a ratio image (e.g., 12C15N/12C14N), it does not look so pretty because there are a lot of noisy pixels in areas where the ion counts are low. Could I overcome this aesthetic issue, for example, by modulating in every pixel the hue, which represents the value of the ratio according to the color map used, in such a way that the hue intensi… text/html 2017-11-15T20:39:23+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:huge_files?rev=1510774763&do=diff Processing of huge IM files 2013-10-26 I have a very large *.im file (>700MB) and my computer does not seem to be able to process it in 'one shot', most likely due to limited memory. Can I process the data in parts, for example by loading only specific masses or specific planes? text/html 2017-11-16T08:34:40+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:last_column_last_row_bug?rev=1510817680&do=diff Circumventing the 'last-column/last-row bug' of *.im files 2017-11-04: When processing an *.im file, I noticed that the images have a strange artifact. Specifically, it seems that the upper-most row and the left-most column of the image are not where they should be, but are instead in the lower-most and right-most parts of the image, respectively. What is this and can I fix it? text/html 2017-11-15T16:11:16+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:pixel_by_pixel_scatter_plots?rev=1510758676&do=diff Plotting ratios in ROIs - pixel-by-pixel in color and as 2D-histograms 2013-01-05: I want to display an x-y scatter plot not using the ratio values derived from ion counts accumulated in ROIs but using pixel-by-pixel ratios values. I want to include only those pixels that belong to ROIs that I have drawn and classified, and I want the data-points in the scatter plot to be color-coded based on the ROI classes. text/html 2017-11-16T05:32:39+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:process_multiple_im_blocks?rev=1510806759&do=diff Merging multiple IM files 2015-06-10: I acquired ion count images from the same field of view (FOV) several times. Now I want to be able to merge these multiple *.im files and analyze them at once. Possible solution * Select Load multiple RAW datasets in blocks from the Input menu of the main LANS GUI. * Use ctrl when selecting multiple *.im or *.im.zip files. * In the dialog window that pops up, specify the block size, i.e., the amount of planes that will be loaded and stacked withou… text/html 2017-11-15T15:47:00+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:remove_rois_based_on_size?rev=1510757220&do=diff Removing multiple ROIS based on size 2013-01-05: I have too many ROIs with size in a specific range and I want to remove them all at once. For example, I want to remove all ROIs that are smaller than 5 pixels. Possible solution Select Remove multiple ROIs by size in the Action menu of the Interactive ROIs definition tool. text/html 2017-11-15T15:44:18+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:rois_logical_expression?rev=1510757058&do=diff Definition of ROIs through a logical expression 2013-01-05: I want to define ROIs (regions of interest) as contiguous groups of pixels that satisfy a certain condition. For example, I want to use the 12C14N image as a template for ROI definition, and define ROIs by selecting all pixels where the accumulated 12C14N- ion counts are larger than 3000. text/html 2017-11-18T05:55:04+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:watershed_roi_segmentation?rev=1510980904&do=diff Watershed segmentation of ROIs 2017-11-04: My nanosims image shows a larger 'blob' of relatively high but quite variable ion counts. Could I use some automated image processing tool, such as watershed segmentation, to segment this pattern into several smaller ROIs? text/html 2017-11-20T13:54:04+02:00 http://nanosims.geo.uu.nl/nanosims-wiki/doku.php/nanosims:lans_extras:working_with_external_images?rev=1511182444&do=diff Working with external images 2017-11-04: In addition to nanoSIMS images, I have imaged the same field of view (FOV) also with another instrument (e.g., fluorescence microscope, AFM, SEM, TEM). I would like to analyze the nanosims and external image data together in LANS. Specifically, I would like to align them, overlay them, extract lateral profiles, define ROIs based on the external image, calculate ion count ratios in these ROIs, plot scatter plots of nanosims vs. external data, etc.