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  • slash - Finding Round Compartments
    with the 3rd mouse button and the numpad keys where 9 and 3 will move the point up and down one slice To see a side view it can also help to open a Slicer window Image Slicer then click the little keep centered icon a box in a box and change the X rotation to 90 to see an XZ view You can also use the 3rd mouse button in the slicer window for even better alignment and centering the point between whole slice values You ll probably also find you want to use the mouse wheel to adjust the radius slightly or you can delete a contour by hitting shift d Alternatively you can deleting a point with del and run Edit Object Clean to delete empty contours at the end Often you ll find that the blue points are almost all wrong so one thing you can do is actually delete that whole object by first selecting that Object Edit Delete When you re happy that all bad points are removed you may wish to merge all the good spheres into the original object The easiest way to do this is open the Name Wizard by clicking Special Name Wizard Here you will see the names of each object including the confidence range values output by imodfindspheres To merge objects just tick all the desired objects to merge then click Selection Merge Selected A more advanced method is to click Edit Contour Move and this will bring up a dialog which lets you move a single contour at a time into any other object something which can help you sort contours into their correct object in cases where you may have more than one type of spherical shaped compartment This next image shows a good setup you can use for the Slicer and Move Contour windows which you can use to quickly adjust and move sort points Looking Deeper In the example above we typed the bare minimum arguments which slashfindspheres allows To see a full list of arguments you can just type slashfindspheres to see the syntax or type man slashfindspheres to see a more in depth discussion of all the options Here s a copy of the syntax usage of slashfindspheres imodslashspheres syntax Usage slashfindspheres options image input model output model Options o list of scattered pt objects to use as input eg 1 4 5 or enter o 0 for no object approach if omitted the program uses the 1st scattered pt object in the model e list of extra scattered pt objects we don t want to overlap G of pixels to use as a gutter around each sphere radius when generating template to match default 2 Z of pixels to use as a gutter in Z default G zScale C cut off for cross correlation as a percentage default 80 R a range of pixel values to scale the cross correlation M maximum allowed pixels for a template to span default 30

    Original URL path: http://longbeach.crbs.ucsd.edu/tools/20-download-tools/imod-plugins/46-finding-round-compartments (2016-02-17)
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  • slash - Interpolator Plugin
    the distance between z slices and complexity of shapes Just as important as saving time the resulting surfaces are much smoother than can be accomplished by drawing every slice Drawing every slice is actually a bad practice because even if you apply post smoothing the resulting mesh will have ruffles and result in a significant over estimate of surface area Features Contours are connected if they are within Z Bridge slices of each other and the computer believes they are part of the same surface as according to the selected surface method The shape of interpolated contours depends on which interpolation type you have selected The types of interpolation available are Linear generates interpolated contours along a fairly straight line between contours using a simple shape morphing algorithm Spherical generates interpolated contours in the profile of sphere and does not deal with branching This type of interpolation is ideal for anything roughly round and unlike the other forms of interpolation you can draw a contour in the middle hit enter and if it doesn t connect to any surfaces it will generate an initial sphere for you to refine Smooth generates interpolated contours such they form a smooth curved surfaces To do this it uses cardinal splines and is quite a basic variation on linear interpolation which takes very little extra processing time In addition to the interpolation modees there are a few useful shortcut keys eg u to toggle a contour between key interpolated without Interpolating g to find a gap between nearby contours or isolated contour h to find a large hole between interpolated contours and under the Actions button are some extra functions actions such as removing regenerating all interpolated contours or changing contour values over a numeric range You can read about all of these features

    Original URL path: http://longbeach.crbs.ucsd.edu/tools/20-download-tools/imod-plugins/47-interpolator-plugin (2016-02-17)
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  • slash - Livewire
    or lines drawn around images from neighboring slices or frames in the case of 3D image data or animation How Livewire Works Livewire typically works as two stage process The entire image must be filtered using filters such as the Median filter and or edge detection algorithms such as the Sobel filter and if not already converted to grayscale such that black regions the smallest value represent the most desirable paths A lowest cost path algorithm is applied to the modified image to find the best path from one point to another In resulting graph each pixels is a node with edges going to the 4 up down left right or 8 pixels around it and the edge costs are defined on a cost function based on the pixel value and possibly other factors How Our Implementation Works In our implementation of livewire the user must first select the nature of the object he s segmenting eg around a dark line around a dark area around colored areas etc and from this a suitable filter and is chosen When the user clicks and area of the image is filtered in a livewire calculator thread and a separate livewire thread thread runs Dijkstra s algorithm over the filtered image to find the lowest cost path from the selected livewire point to the mouse To increase user efficiency a second livewire calculator shows the lowest cost path wrapping back to the first live point allowing the user to double click to complete the contour In the version we ve implemented in IMOD the user can also click and drag out intermediate points to refine the contour and a special yet unpublished algorithm used to help optimize and weight contours in adjacent slices allowing for faster results in 3D How to Install Use

    Original URL path: http://longbeach.crbs.ucsd.edu/tools/20-download-tools/imod-plugins/48-livewire (2016-02-17)
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  • slash - Name Wizard Plugin
    what other compartment types can help eliminate false positives etc Giving ALL objects consistent and PROPER names names taken from a shared vocabulary is critical because without this nobody in your group let alone any computer database or collaborator outside your group will be able to identify compare understand analyze data mine or share your model file and odds are your model will be deleted after you leave To learn more about the important of using standard names read this article on naming objects in IMOD Naming Authorities What one person may accurately name Mitochondrial Outer Membrane another may name Mitochondria mitochondrion Mito memb MITO23 MT dark thing green or just leave blank The idea of this plugin is to discourage people from making up names and or leaving objects unnamed The names you use should instead should come from an authority website such as The Gene Ontology or Neurolex Neuroscience Information Framework NIF Features In addition to naming objects correctly this plugin can also be used to reorder merge delete and duplicate objects Probably the nicest feature however is the use of auto complete to quickly enter and verify names To facilitate fast loading candidate names are stored in a comma seperated value CSV file Entries in this file were taken from Nuerolex s subcellular parts table and you can easily add your own names and standard colors for your group to use since not all IMOD users are in the life sciences For more information about this plugin s features you can read the Name Wizard Help documentation here Instructions to Install The stereology plugin was added to standard release of IMOD in version 4 3 in 2001 To install the latest version Go to the IMOD download page download the appropriate version for your computer Follow the

    Original URL path: http://longbeach.crbs.ucsd.edu/tools/20-download-tools/imod-plugins/49-name-wizard-plugin (2016-02-17)
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  • slash - Stereology Plugin Introduction
    back to these models later to check points and or add points to the grid What is Stereology Stereology originally defied as a the spatial interpretation of sections is a technique for 3D interpretation of 2D planar sections of materials or tissues To achieve this stereology uses a random sampling and systematic approach to provide unbiased quantitative data Put another way stereology exploits the fact that many 3D quantities can be determined without 3D reconstruction for example the 3D volume of any object can be determined from the 2D areas of its plane sections In the fields of cell biology and electron microscopy stereology allows scientists to estimate the volume number and in some cases size of cellular compartments by looking at a relatively small number of 2D slices and unlike the notoriously slow techniques of 3D reconstruction and segmentation allows scientists to attain these estimates very fast As such stereology is is a technique all cell biologists should know or better yet become familiar and experienced with Due to it s rapid nature one day of counting is often enough to generate an entire table of results and the fact that stereology can be done live on a microscope no saving or storing of images required or using existing 2D and or 3D images of cells images which have already been collected stereology is a brilliant compliment to slower methods of 3D analysis Stereology can scale over any size dataset the important thing is a the number of points b that you re points are spread over a wide area and c you points don t have a bias eg by being in a different region from one specimen to the next typically 1000 points gives good statistically accuracy and takes under an hour By counting 1000 points in three different specimens of wildtype then three different specimens of condition X you have publishable statistics which can quickly support or reject a hypothesis and help you decide if you want to invest the time for segmentation Features To speedup the process of counting points faster than is possible with manual counting recording of points the plugin allows you to classify points using shortcut keys navigate the grid with arrow keys and also has a special Point Painter where you can quickly paint regions of points a particular color In addition to this you can apply rules or use closed contours to apply masks change the value of multiple points or automatically add interception points for estimating surface area with test lines Although not originally designed for stereology the advantages of using IMOD s 3dmod interface to segment perform stereology is that 3dmod has a great set of tools for viewing and navigating 3D images and you are able to show and perform surface segmentation and point counting within the same model Before using this tool however you should make sure you understand the Basics of Stereology click to read The Stereology plugin specializes in point counting stereology but if

    Original URL path: http://longbeach.crbs.ucsd.edu/tools/20-download-tools/imod-plugins/50-stereology-plugin-introduction (2016-02-17)
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  • slash - Stereology Plugin Tutorial
    forgotten to add if she hadn t browed a few points before locking ht her categories Each category will map to a number shortcut and it makes sense to place the most common categories first In this case the myelin and axons are very common so Christine has put these as category 1 and 2 and the least common categories are at the end To change the color of a particular category click the colored button on the left No matter how many categories you have we always recommend you leave category 0 as NO CATEGORY Category 0 will maps to the number 0 on the keyboard and is useful to classify any points which fall outside the useable area or might be inside organelles that you cannot identify had not anticipated and or simply don t want to include in your final analysis Before finalizing the categories you ll probably want to save these categories as the new default To do this click the little down arrow below your categories and save categories as new default as per the image This will help make sure you prevent any confusion and use the same list of categories numbers colors and names on each dataset To lock in these categories click Finalize Categories Note there is a option here allow multiple categories per point you will leave unchecked If christine had made just one option for mitochondria she might need to check this option to help specify that a mitochondria might belong in either an astrocyte or an axon but it s much easier to count points if you don t have to check this option Click Finalize and you are now ready to start classifying points You ll notice that the Stereology plugin will add a certain number of objects to your model the first of these which is probably object two stores the parameters of the grid and list which points you have checked and after that is an object for each category You should never alter these objects deleting points adding contours etc unless using the Stereology plugin Now is a good time to save your model file Go Menubar File Save as It helps to save the model with a name that matches the image file and don t forget to add a mod extension Christine has saved this dataset as opt WT1 stereology mod TIP If you re comfortable with IMOD and all your images are exactly the same size you might consider using this file as an empty template simply copy the file multiples times eg opt WT2 stereology mod and this will allow you to quickly start each new stereology set Step 6 Classify all Your Points The type of stereology used in this example is called point counting stereology It s called this because typically you count the number of points in each category and write them onto paper Here we are getting the same outcome but instead of needing to count you will instead just classify each point Before you start classifying you should zoom in far enough use the key that it s easy to clearly distinguish what type of category the selected point falls into This very first point pictured below is inside an axon To mark it as such you can click the push button Axon but what works much faster is if you quickly learn the number keys and use these Each time you press a number that point gets marked as checked and you ll automatically be taken to the next point An important rule in stereology is on the line is considered in just like in tennis In the example below the point is on the mitochondrial membrane and thus considered in so Christine will press 5 to put it into the appropriate category In cases where a point is unclear don t forget your dataset is in this case at least three dimensional so the PgUp and PgDown keys can be used to scroll to adjacent slices and help identify any unclear blurry organelles Hopefully it will only be a very small negligible fraction of points you cannot clearly identify and so it won t matter if you take an educated guess or use NO CATEGORY If you accidentally mis categorize something you can use the right arrow key to go back or even left click a point to jump to that point and simply change the category Extra Features Checking estimating progress Counting points should go pretty quickly but if you want to check your progress and see how many points are in each category you can click Options Check progress This popup will show you how many minutes you ve spend classifying pressing buttons and estimate how long it will take to finish Depending on your image and number of categories you might count your first dataset at about 1 point per 3 seconds 1000 points hour but get a bit faster the more you count Don t try going too fast Changing colors and appearance If you are unhappy with the color or appearance of categories you can use the up down arrow on the main IMOD window to select that object and then go Edit Object Color For even better control go Edit Object Type and you can change the sphere size or also set a symbol size In Christine s setup notice she has change her objects so that certain objects are represented with square and triangle symbols To change the color and or appearance of the stereology grid itself click Options Display Options Point painter and contour masks In cases where you have large 2D areas of all the same category or of no interest you may consider trying the point painter To use this feature click the Pt Painter button use the mousewheel to change the size of your paint area and hold the appropriate number key to paint all points inside the area the right color Another

    Original URL path: http://longbeach.crbs.ucsd.edu/tools/20-download-tools/imod-plugins/51-stereology-plugin-tutorial (2016-02-17)
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  • slash - WIB: Feature Outline
    html js wav mp3 eps ppt pps swf tar tex gz slash Tools Support Discover About Help Search Search WIB Feature Outline Controls Shift drag for pan Control click for select current contour and object z and x to adjust circle size zoom out zoom in Advanced drawing tools Sculpt Nudge with variable sized circle Set location Ability to go to x y z location at given zoom using url

    Original URL path: http://longbeach.crbs.ucsd.edu/tools/25-download-tools/wib/52-wib-feature-outline (2016-02-17)
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  • slash - SLASH IMOD Stereology Plugin Added
    Support Discover About Help Search Search SLASH IMOD Stereology Plugin Added To help expedite analysis of data we have built a special SLASH Stereology plugin into IMOD to allow user to rapidly gain estimates of the compartment volumes number and even surface area The plug contains many built in grid uniform grids physical dissector line pairs cycloids rectangles and so on pictured below This plugin became part of the IMOD

    Original URL path: http://longbeach.crbs.ucsd.edu/slash-imod-stereology-plugin-added (2016-02-17)
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