Angler: A C.elegans Embryo Development Browser in Time and Space Angler V1.0 21/10/96 Clive G. Brown . cgb@sanger.ac.uk Informatics Group. The Sanger Centre. Hinxton Hall. Cambridge. UK Angler is a viewer for a 4D image series of C.elegans embryonic development. It comes with a database of Nomarski images of wild type development taken at a series of 25 focal planes at 16 timepoints up until 230 minutes of development. This is a subset of a larger data set that was captured in Ralf Schnabel's lab in Martinsried, and annotated by Harald Hutter to assign all the cells and hence connect them to the embryonic lineage. The purpose of Angler is to enable biologists to be able to browse these data starting either from the images or the lineage, highlight and follow specific cells, and export annotated images to other applications. Both Macintosh and Win32 versions of Angler are available. The Win32 version should work under either Windows95 or Windows NT on Intel workstations. Getting Angler To get Angler you need to transfer three archive files, one containing the program, one containing the database and one containing a set of files for the system folder of the given platform. Instructions on downloading and installing are available in a "Readme" file on the Sanger Centre ftp site and in the above archives. You can transfer them either using the file transfer capabilities of a Web browser from (http://www.sanger.ac.uk/~cgb ), or an ftp program such as Fetch. Different versions of the archive are needed for Macintosh and PC. Copies of the Readme files are appended to the end of this document. Macintosh: When the files are unpacked you should have a folder called "Angler" which contains a sub-folder called "Database" which in turn contains a folder called "images". Inside the Angler folder is the application itself called Angler (there is also a version for older 68K Macintosh called Angler68K). There are also some miscellaneous files. Inside the database folder are a set of files with ".db" extensions and the "images" sub-folder. These must not be moved or altered in any way. In the images folder are the actual embryo image files. The file names contain the time in minutes and the focal plane of the given image. These filenames must also not be altered. PC (Win32 on x86) Instructions for getting the three windows archives ar contained in a Readme file on the Sanger Centre ftp site at : ~ftp/pub/cgb/Angler/Win32. This Readme is also appended to the end of this document for reference. General To run Angler, double-click on the Angler application icon. After a little time (depending on the speed of your machine) you will see a window. This contains an image of a four cell embryo; we will call this the Main window. If you click on the "tree" icon on the application toolbar or choose "Cell Fates" from the "View" menu then a second top level window appears which contains the cells' lineage's and related data, we will call this the Cell Fates window. The two windows are coupled. For example, if you click on one of the cells in the image on the main window, the corresponding cell name is highlighted in the cell fates window. We will describe the primary features of each window in turn. Main window Image: The main window contains the current image. If you click in the image then the nearest cell is selected. When this happens its name is shown in a box at the bottom of the window, and also in the Cell Fates window. Note that Angler picks the cell whose centre is closest in three dimensions. This may be one that is further on the screen, in the x and y dimensions, if it is closer in depth. Also a list of recently clicked cells is stored and view in a List Box on the Main window. Sliders: Below the current image there are two slider bars, which allow you to control the time point and focal plane, or depth, of the current image. The boxes above these sliders show the current values. Co-ordinates: To the right are two more boxes showing the co-ordinate position of the cursor when it is inside the image. This can be useful for making measurements, such as tracking movements in time. The co-ordinate system used corresponds to that provided by Hutter and will map directly onto the pixel co-ordinates of the original images. Overlays: Below the co-ordinate boxes is a check box labelled "Toggle overlays". If you check this, then a colour overlay is generated, showing the location of cells at this time point. Cells are coloured according to a colouring scheme that you can change via the Cell Fates window. If a current cell is selected, it is highlighted in bold, and a small white arrow is drawn indicating its position. Also if the Cell fates window is visible the cell is highlighted here. If you turn on the overlays on the initial image, each cell will be indicated by a cross and a small circle. As you move down in focal plane, the circles get bigger as you approach the centres of the corresponding nuclei, then smaller again. If you move forward in time then there are more cells in the embryo, and any one cell is only visible on some of the focal planes. The approach we have taken for the overlay is to draw a small cross for all the cells at the current time point, and then to calculate a conceptual sphere around the centre of the nucleus. If this sphere intersects the current focal plane, you see a circle. Therefore whether a circle is present, and its size, indicate how far you are from the focal plane of its centre. Menus The Menus on the Main window allow you to print and print preview the images. Also you can copy the images to the clipboard. Short cuts for the menus are provided by way of buttons on a docking toolbar seen at the top of the main window and by keystrokes. Cell Fates Window This is shown or hidden by choosing the menu item "Cell Fates" from the View menu or by pressing the "tree" toolbar icon. This Window floats above the Main window and contains a tree of cells and their daughters as well as showing the colours of the cell overlays. Cells without a colour on the tree cannot be seen in the image data set, usually because they are pre or post the range of the image dataset. Clicking on cells in the tree causes them to be selected as the "current cell". If that cell exists in the main window image it is highlighted. Information about the currently selected cell in this window is shown above the fate tree. There are also two buttons here labelled "Locate Current Cell" and "Find Cell". Pressing Locate Current Cell moves the image in the main window to the time point where the given cell first become visible and to the focal plane on which the given cells' centroid lies.. If the cell already exists time point currently shown in the main window when the button is pressed then the main view simply adjusts to the focal plane of the cells centroid at this time point. The Find Cells button produces a dialog box of cell names .Double clicking on a cell name selects it, pressing the OK button finds and selects that cell in the fate tree. If you then press the Locate button the main view will adjust accordingly. Menus. The menus on the Cell fates window allow the tree to be fully expanded or collapsed. "Find Cell" is duplicated here. Under the "Options" menu you can select subsets of the fate tree. If you select "Browse from P0" the whole lineage set is chosen starting from P0. Choosing "Show All Cells At This Time" selects cells which exists from the current time point onwards. There is a toggle switch on the Cell fates window labelled "Auto track". When this is toggled "on" the current data subset in the Cell fates window keeps track of changes in the main view. Thus if the current subset is the cells at the current time point and one then changes the time point in the main window then the Cell fates window updates its dataset accordingly. In the "options" menu is a sub-menu which allows cells and subsets of cells to be differentially coloured. This is done by selecting the cells in the fate tree and changing their colours using a colour choosing dialog box. Overlay colours in the main view are kept up to date with these changes. Known bugs We are missing all the images from the 144 minute time point in our current data set. These have temporarily been replaced with test card images! Network locations of Angler Angler can currently be obtained from ftp://ftp.sanger.ac.uk/cgb/Angler/ http://www.sanger.ac.uk/~cgb feedback to : cgb@sanger.ac.uk **************************************************************************** ** Angler v1.0 BETA RELEASE * **************************************************************************** **WIN32 VERSION** To run Angler on an x86 PC you must have a Win32 operating system, such as Windows NT or Windows 95. It will use up around 5 MB of RAM (more if it available), and you will need around 250Mb of disk space for the images. You need to get 3 files in binary mode: 1) Angler_database.ZIP - the database of images 2) Angler1.0.NT.ZIP - application etc. for Windows NT 3) Put_in_System.ZIP - system addins You must put these in a directory called C:\Angler on your C: hard drive. They must be unzipped using WinZIP6.0 or higher, which is available from many sites. Files from (1) will create a folder called Database which will contain a bunch of binary and text database files and another subfolder called images which contains the embryo image data files. (2) will give you the application file and some more files for Database. Files extracted from (3) should go into the Windows System32 directory. You may need to respecify the name of this directory when you extract with WinZIP if you have renamed your Windows folder. To run Angler, double click the application in file manager, or drag the program file from File Manager into a program group on your desktop and an application icon will appear which you can double click... For instructions on how to use it, get and read Angler.doc. This is a beta release test version. We expect it to have problems. Please mail me if you install Angler, so I can keep you informed about new versions, and PLEASE send comments/bug reports back to me, including any problems with installation. It won't get fixed unless you tell me what is wrong! Clive Brown cgb@sanger.ac.uk 21/10/96 **************************************************************************** ** Angler v1.0 BETA RELEASE * **************************************************************************** **MACINTOSH VERSION** To run Angler on a Macintosh You will need 5Mb of RAM available for the application, and around 250Mb of disk space for the images. You need to get 3 files in MacBinary mode: 1) Angler_database.sea.bin - the database of images 2) one of Angler1.0.PPC.sea.bin - application etc. for PowerPC macs Angler1.0.68k.sea.bin - application etc. for 68k macs 3) put_in_system_extensions.sea.bin - system folder addins These should all be put into a new folder on your hard drive, and double-clicked to self-extract. Files from (1) will prompt you to create a folder. This folder (you name) will contain a subfolder called Database which will contain a bunch of binary and text database files and another sub-folder called images which contains the embryo image data files. (2)Will unstuff with the default folder name "Angler_PPC", you can change this to anything you want. Inside this folder is the application file and some more files for Database. Files extracted from (3) will appear in a subfolder called Put_in_system_extensions. Having unpacked the archives into the three folders 1. Put the files in the Put_in_system_extensions folder into your System:extensions folder 2. Make a folder called "Angler" and move the CONTENTS of the folders you created when you unpacked the other two archives into it. You now have a folder called "Angler" on your hard drive. Inside this are some documents and the application executable. There is also a subfolder called Database inside which are the .db files and another subfolder called "images" which contains the image files. To run Angler, double click the application icon and the program will start up in a few seconds.... For instructions on how to use it, get and read Angler.doc. Memory requirements: Angler will run happily in 5Mb of RAM, which is what is set in the distribution version. However, if you have more memory available, then Angler can make use of it. If you allocate more memory from the "Get info" window, then Angler will hold more images in memory, and so back-and-forth image operations such as moving up and down in focal plan will be faster. This is a beta release test version. We expect it to have problems. Please mail me if you install Angler, so I can keep you informed about new versions, and PLEASE send comments/bug reports back to me, including any problems with installation. It won't get fixed unless you tell me what is wrong! Clive Brown cgb@sanger.ac.uk 21/10/96