MAPaint User Manual and Help Pages
Contents
1. The anatomy menu becomes available when a Theiler stage is selected from the file menu The anatomy is read on from the Edinburgh Mouse Atlas CD ROM and is a menu version of the anatomy 5 THE USER INTERFACE 16 hierarchy defined in the database The anatomy database is a standardised anatomy nomenclature arranged as a tree hierarchy Each anatomical component in the tree represents a subdivision of its parent component with the root of the tree being the entire embryo plus extra embryonic tissues deemed to be of interest for gene expression studies in development Each tissue which is further subdivided shows a pullright arrow to the right of the tissue name Absence of this arrow implies no further subdivisions Some of the tissues in the tree have been delineated as a 3D domain in the reference image In this case the tissue name will appear at the top of the list of the pullright menu with the word domain appended and it will be separated from component tissues by a line in the menu The anatomy list represents all the tissues that are present during the developmental period defined by the stage The painted domains are those that are recognisable in that particular reference image which is a snapshot within the range and therefore will not in general have all tissues present Furthermore not all tissues are recognisable or distinguishable within the resolution of the atlas and have therefore not been defined For these reaso2. M Filter ard MouseAtlas sre MAPaint sre wlz Directories Files PO 0 da oz 54 MAPaintSectObj wlz reconstructions msxi wlz que wlz small wlz surface wlz El pem Woolz 4 fill blanks M min domain Selection richardMouseAtlas src MAPaint src OK Filter Cancel Help When Read Object or Write Object on the File Menu is selected then a file selection di alog will be displayed By default the files will be filtered for file extensions of the form wlz because woolz image files are the default format Other formats are available from the pull down menu A file can be selected by clicking on the file name in the file list widget and the image read by pressing the Ok button The directory can be changed by changing the directory string in the filter or by selecting a directory in the directory list then pressing OK Double clicks in either the file or direc tory list will result in the file being read or the directory changed respectively For the paint program the woolz object must be of 3D type and must have a voxel table 27 In addition to the image format pull down the read file dialog has two toggles to control the behaviour of paint with respect to reference images with blank planes If fill blanks is selected then then a blank domain with grey values set to the background value will be inserted for any empty plane of the reference imag
3. Controls Auto increment Propogate domain 1 wlz domain 2 wlz domain 3 wlz Read domain domain 4awlz Write domain domain 5 wlz Clear domain domain wlz Display 3D domain domain 7 wlz Clear all domains M domain_ wiz Write painted volume domain 18 wlz e Controls lows the user to select the current domain for any of the domain operations paint read write and clear If a domain is cur rently being painted then a new selection for painting will only take effect after that paint session is over The effect is immedi ate for the other domain operations The cascade menu is a set of radio button tog gles in which exactly one is set at a time The currently selected domain is shown by the state of toggle indicator by default red The domain mask is not currently implemented but can be emulated by us ing the the highest dominance domain as the domain mask 17 5 THE USER INTERFACE 18 1 2 s 5 UN m sj 6 Ok Cancel Help Selecting Controls will popup the domain controls dialog above which can be used to modify the dominance hierarchy The dominance ordering is left to right on the displayed list as indicated by the numbers This ordering is also reflected in the Select menu i e the domains of higher dominance are higher up the list To change the dominance ordering select and drag the do
4. domain 5wiz ETE domain s wiz Greys domain 3 wlz TNT domain wlz domain 1 wlz_ domain 1 wlz domain 4 wlz Review Stop ome Help The purpose of domain review is to allow the user to scan through the component parts of an input domain allocating as required to different paint domains including clear to grey and ignore i e leave existing domains alone The dialog is divided into four regions plus the action button bar at the bottom The four regions are Source domain use the controls to select the source of the domain for review The Source choice menu allows selection between Review domain MAPaint domain and Read domain When new domains are read in from the Read domain option of the Domain menu the new domain is checked against existing painted domains If there is overlap then the user can choose for the intersection region to be installed as the Review domain for later review This will be used as input to the review process if the Source selection is Review domain 5 THE USER INTERFACE 33 The MAPaint domain choice means tha an existing paint domain as determined by the MA Paint domain choice box can be used as input for review Finally the Read domain option activvates the Read button to allow a domain 2D or 3D to be read from disk Review planes Once a domain has been installed for review if it is a 3D object then the planes of that object will be listed within the Review planes control area This is to all
5. Under certain circumstances domains erased this way could be recovered from the autosave file e Write Painted Volume This option was put in to allow MAPaint to serve as a means of generating prepared volume images for volume rendering in other 3D visualisation systems e g Sunvision AVS Express Volvis and VTK It can also serve as a quick save of all painted domains which can be recovered by reading in the painted volume as an autosave file 5 2 4 View Menu E A gt gt n ean File Anatomy Domain View Options Misc Help X view Selecting any of the view menu entries will pop up a view dialog showing a cross section of the 3D image and providing a full set of controls for modifying the viewing parame Y 2 view ters For more details see the sec view dialog The 3D images are defined as a stack of planes with an x y z co ordinate frame defined so that the x y co ordinates are within the plane and z is perpendicular to the planes A view of the data 5 THE USER INTERFACE 20 is defined by a viewing direction two angles in 3D a fixed point in the original co ordinates and a distance parameter d The viewed plane is defined to be perpendicular to the viewing direction and the perpendicular distance from the view plane to the fixed point is d For details of how the 3D viewing plane is transformed onto a 2D window see the paint reference document All the viewing parameters can be adjusted
6. age format for MAPaint http genex hgu mrc ac uk Software woolz ICS ics ids Standard for Image Cytom etry Data Files Cytometry 11 1990 561 569 Stanford Density den http white stanford edu Sunvision vff 3D voxel format for Sunvision now incorporated as part of AVS Ex press BioRad Confocal pic 3D format for the BioRad confocal microscope VTK vtk Native format for the Visualisation Toolkit http www cs rpi edu martink SLC slc Netpbm pgm Pixel grey image netpbm standard 3D image are written as an enumer ated series of 2D images Bitmap bmp Microsoft bitmap format 3D image are written as an enumerated series of 2D images If other image formats are required then use e g netpdm tools or the program convert from ImageMagick 5 The User Interface MAPaint has been implemented in C with the X11 GUI implemented using the Motif widget set to provide a standard look and feel Where the user interaction has had to be implemented directly in X11 the Motif style has been followed if possible 5 THE USER INTERFACE 5 1 Main Window l File Anatomy Domain View Options Misc Help The paint program main window follows the standard Motif layout style of a menubar pro viding the pull down menus a work area which displays a 3D representation of the cur rent domains if requested and view planes and a button bar for commonly u
7. Das Doman Surgery Dialog sic aa ROXOX XR R on EUROS e deem OG Ro 34 5 8 9 Autosegment Dialog llle 34 GIO Colormas Dialog crossover o RR xod RN E Ro ORO RR x 35 Gall Autosave Dialog ss o o Eoo Roe ook RR EGER REOR ER 36 Using a Graphics Tablet less 36 6 1 Installing WACOM tablet lle 37 6 2 Generating Printed Views llle 37 6 3 Calibrating the Coordinate Mapping 22e 37 CONTENTS 7 Painting Techniques and Strategies aa less 8 Conditions of Use oo ccsa cos ooo o RU E 3 REOR RR ORE RUE RS 9 Version 1 INTRODUCTION 1 1 Introduction The HGU paint program has been developed for the special purpose of painting or segmenting an arbitrary 3 dimensional domain within a given 3 dimensional voxel image The basic idea is that the user can view a slice of the underlying voxel data at any arbitrary position and angle In fact there can be as many such views displayed simultaneously as are required see the Views Menu Each view displays a number of voxels from the underlying reference image and the user can mark or paint the voxels as belonging to the domain of interest As soon as the voxels have been painted in one of the views then they will show as painted in all other views if visible By updating the view and continuing the process it is possible to define an arbitrary 3D domain within the reference image It is possible to delineate more than one domain
8. EE 7 00 X size Y size 5 3 3 Read Write Domain Dialogs Read 3D Domain Filter rd MouseAtlas src MAPaintsrc wlzx Directories Files 9 dau wlz is MAPaintSectObj wlz reconstructions msx1 wlz qwe wlz small wlz surface wlz richard MouseBtlas src MRPaint src The properties dialog provides information about the reference image and allows a num ber of parameters to be set The background property affects the way empty regions of the reference image are displayed and the voxel sizes X Y and Z size will change the voxel size property This will not affect the dis played reference image in this version of paint but will make a difference to the saved do mains when viewed in for example AVS If the changed properties are required to be set in the reference image then the reference im age must be written to disc 29 5 THE USER INTERFACE 5 3 4 Write Painted Volume Dialog Write 3D Painted Volume Filter rdMouseAtlas src MAPaint src wlzx Directories reconstructions 9 dau wlz MAPaintSectObj wlz mex1 wlz qwe wlz small wlz surface wlz Select image type Woolz Selection richardMouseAtlas src MAPaint src 30 5 THE USER INTERFACE 31 5 8 5 View Dialog Section filled 3D view view direction 215 146 152 250 cardiac jellu greys The view dialog shows a 2D section through the 3D image data Th
9. PURO S RO oor 3L CONTENTS ii 6 1217 A amp ubosave Dialog ogc ek 29 a RR Red Ea RS RC RS ELE ES 10 43 Input Data Formats 20 xo oo ee E oo on Re Re x Re mok oh wu OX E OR ES 10 44 Output Data Por 012242 29309 Roo 9 om a Rn es MESE ek o 11 The User Interface sene 12 Od Mam Widow oe e Que 39 xh Be XR BUE x Oe ee dion 13 Oil 3D Display lt s gt se sa 9o ce Abba eee Ae Be EEG eS 14 5 2 Pulbldowu MenuB e sa saa 45 45 25886 a eee ES a ee Be 14 5 21 File Ment 2 cos co eed Ge hae ee o3 9 OR EER eG we oe 15 5 2 2 Anatomy Ment e se saw amad 248 ds we Ee RE ne ee 15 o0 Domain Ment oa ae oe A ea ew ae A ox ae a SAR we oe 17 9 4 View Ment lt o raa eee iS 4d oec Sa X94 4 eS ee Rex Kudos 19 uxo prons Moni nk rae g gt he ee a SOSA RO A A E RR NA e 20 wc Mibo NENI soea koe eo p dee x ek E e ee ee BY OE 25 mor Mocro K eenaa qt che BO ON Se UR que AE Ge ORE EX 25 eee Help Momu sec ate Boe yra he eH a d a eee el we ee SY ee 26 ee CAI ag aA borg gee Amok a gt hed doer eek AR A TIT 27 5 3 1 Read Write Reference Dialogs o 27 5 3 2 Reference Properties Dialog o 29 5 3 3 Read Write Domain Dialogs 2 3 lt 0 05 eA Ree Se e 29 5 3 4 Write Painted Volume Dialog o namatia 30 bolo OW TG 2 bolo e p how RO eh a Reano 31 bano Tools Controle Dialog a s siii el aera knd G E Roe E hem OS wa 32 5 3 1 Domain Review Dial g beea araa ara m wee x Roe xm Xp Ron 32
10. Re ee a 3 Installing MAPaint oe zz sso zoo oo yo UR OE E Re rex 3 1 System Requirements 2 2 2222 ls zm s sh n ose 3 2 Obtaining the Program 2 2222 ooo be a Eo REOR x RO da o Installation i252 s 085806 22542 bee dy BOO OR OE XOR ERG E x RUE o 4 Running MAPS seos e 65042 4 a e XE hex Eos E ESAE C RUD UE E Ae Ua os 4l Command line Arguments 2 4 55 0584 22 xr o ox a ee we 42 RITRO e Louoe amp exem es n hok Rex p wok PO A AR qoe eae dre mo A 4 2 1 Behavior and Layout Resources 2222s 4 2 2 3D View 3D Section and OpenGL options 423 File Mena oko cx OW E Ron x 3 RORCRG 4d me ee RO XE x xps 1241 Anatomy Mem oak zc X ow x eu 4o Row 4 404 ep k Xo BeXe dox 4o Aza Domain Meme gt cas mk koe ow Pee Re Re coe ee X XO XE Ro 42b View Me uus zoe mex poea X ow Rok ok ox Re A Re E RA Ag Options Menu lo rosse daa ox eee wed Xem ea ee la dps 4 2 8 Miscellaneous Mena 0 lt lt moe RR RR x Ago Help MEG wg uoo oko 9 OR Pea de eee GE ed RE E ee ee ER dos L2 File Dalt ee gk seo a a RRS Oe He E Y RSS ES R On 4211 Domain Dialogs o ee oe o Ea o EORR ed XS RR SR R X E Ro xo 12129 View Didog so s ke so Ow osos Rom Rom Reed YS E ROS ROO X REOR Xo 4213 Tool Controls Dialog s soes as Ea o Reno ed Xe Rok o O XE SR xo 42 14 Domain Review Dialog lt oo iv ko Rak E S ORE SR x 42215 Surgery Dialog gt e ko oes nos Xo omo e do Po ROS A qe ones dom ce Eu d 42 16 Colormap Diae 22 uomo oko PR R
11. all planes and all parts within each plane if Segment domain is selected offering each part for review by flashing the region on the section view window If a new plane is selected then the review will continue from that plane onwards Pressing Review will popup the required section view e Stop Stop the review process and popdown the section view e Dismiss Stop the review process and popdown the Domain review dialog e Help Probably does nothing If the source domain read from disk is a 2D image then it is assumed that the user wishes to map this domain onto an arbitrary section through the reference image In this case the user is prompted to set the view section as required then can continue to review in the usual way 5 THE USER INTERFACE 34 5 8 8 Domain Surgery Dialog Source domain MAPaint domain Surgery option section cut Discard GE domain 5wiz TEE S domain s wiz Greys domain 3 wlz NITE domain wiz mST domain 1 wlz domain 4 wlz Cut Stop Dismiss Help The basic idea with domain surgery is that the user defines a source domain and a method of cutting that domain in 3D The user is then presented in the 3D feedback window with a flashing display and can assign that region as required using the Destination domain buttons Currently the only Surgery option is to use a section plane determined by a view dialog For this option the user adjusts the view controls of a
12. behavior work_area allocateBackground True work_area background black work_area allocateotherColors True work_area installColormap True HGU_DrawingArea visual PseudoColor HGU_DrawingArea depth 8 HGU_DrawingArea background white 4 2 3 File Menu Resource Default Comment file_menu labelString File file_menu mnemonic F file_menu borderWidth 0 file menu new obj labelString New file menu new obj mnemonic N file menu read obj labelString Open reference file menu read obj mnemonic O file_menu write_obj labelString Write reference file_menu write_obj mnemonic W file_menu obj_props labelString Ref properties file menu obj props mnemonic P file_menu theiler_stage labelString Theiler stage file_menu theiler_stage mnemonic T file_menu theiler_setup labelString Theiler setup file_menu save_state labelString Save state file_menu save state mnemonic S file menu restore state labelString Restore file menu restore state mnemonic R 4 2 4 Anatomy Menu Resource Default Comment anatomy_menu labelString Anatomy anatomy_menu mnemonic A 4 2 5 Domain Menu Resource Default Comment domain_menu labelString Domain domain menu mnemonic D domain menu borderWidth 0 domain menu select labelString Select domain_menu select mnemonic S domain menu select border Width 0 domain menu controls labelString Controls domain menu controls mnemonic C domain_menu auto_increment labelString Auto increment domain_menu auto_increme
13. for any view but this menu provides a number of predefined viewing angles The entries correspond to viewing along the three co ordinate axes z x and y respectively however each view can of course be set to arbitrary viewing angles and positions Full details of the viewing coordinates and the geometric formulae to switch between reference image and section coordinate systems are given in the paint reference document 5 2 5 Options Menu Eo File Anatomy Domain View Options Misc Help The options menu provides all the methods for painting and otherwise editing the do mains The primary mechanism for defin Paint tools 2D ing a domain is by using the 2D tools on a Paint tools 3D plane by plane basis These are detailed be low with further detail given in the the sec tools controls dialog Domain review A few 3D methods for domain are editing re view and surgery as well as options for the display colormap and autosave Tool controls Domain surgery Auto segment Colormap Autosave e PaintTools 2D http genex hgu mrc ac uk Software paint paint paint html 5 THE USER INTERFACE 21 This is a pull right cascade menu which Paint tools 2D pa allows the user to select the current 2D A a painting tool The basic tools are draw Paint tools 2D cs and paint ball which allow the defini Tool controls __ Paint ball tion are arbitrary 2D domains by draw AAA ing arou
14. preferences files except X11 resources therefore has no mecha nism for restoring a previous session automatically In due course this may be possible via the Save Rstore facility but this must be set and recovered by hand 4 RUNNING MAPAINT 4 4 1 Command Line Arguments Apart from X11 resources including all the application specific resources below which can be set with the xrm flag there are only two additional command line arguments Synopsis MAPaint X11 arguments reference image feedback image gt Options reference image woolz format grey level 3D reference image feedback image woolz format image to generate the 3D feedback 4 2 X11 Resources There are a few resources to modify the behavior of paint a few more that modify the layout and a large number that simply define the menu labels etc These are all listed below with the resources likely to be of most interest in the first section This list represents the fallback resources list encoded in the program Note if these resources are to be used in the users XDefaults or XResources file each listed resource name must be prepended with MAPaint 4 2 1 Behavior and Layout Resources Resource Default Comment geometry 258x332 autosaveTime 900 Autosave can be switched off only when the program is running autosaveDir tmp Save directory for the autosave file Set to tmp for efficiency on Solaris machines tmp is memory mapped but
15. section view until it corresponds to the required cutting plane That view should then be selected for painting and then the Cut button is pressed The selected domain as determined by the Source domain choice is then spilt into two parts one on either side of the cutting plane and presented in turn to the user as flashing regions in the 3D display The user can then select the destination domain for the flashing region including reset to grey and discard which leaves that part of the domain unchanged 5 3 9 Autosegment Dialog Not yet implemented 5 THE USER INTERFACE 5 3 10 Colormap Dialog Gamma 1 Low _ d High 1 253 invert Selectoverlay 1 Red NIE 255 Green G Blue Contrast 0 25 The colormap controls allow some manipulation of the dis play of the grey level image and midification of the colours for each overlay In the case of the wash overlays there is also con trol of the relative contrast of the grey to colour A contrast value of 1 0 implies solid colour a value of 0 0 implies no colour 35 The controls Gamma Low high and invert allow modification of the grey value look up table Image grey values within the range low high will be mapped onto the display values 0 255 with lower values mapped to zero and higher values to 255 The mapping will use the value of gamma set which by default is linear gamma 1 0 The look up table can be inverted by selecting
16. size labelString Box file type woolz labelString Box file_type ics labelString Box file_type den labelString Box file_type vff labelString Box file_type pic labelString Box file_type vtk labelString Box file_type pgm labelString pattern restore_state_dia og pattern 0 False Write 3D ReferenceObject wlz Select image type 0 False Object Properties 4 4 Bounding box Planes z Lines y Columns x 0 100 0 100 0 100 Voxel parameters Background X size Y size Z size Woolz ICS Stanford Density Sunvision VFF BioRad Confocal Visualization Toolkit VTK pgm rsc rsc Resource Default Comment helpDefaultUrl paint 1 0 paint html helpIndexUrl paint 1 0 paint html index helpVersionUrl paint 1 0 paint html version help menu labelString Help help menu mnemonic H help menu borderWidth 0 help_menu on_program labelString Paint help menu on context mnemonic P help menu on context labelString On context help menu on context mnemonic c help menu on_windows labelString On windows help menu on_windows mnemonic w help menu on keys labelString On keys help menu on keys mnemonic k help menu on keys sensitive False help menu index labelString Index help menu index mnemonic I help menu on help labelString On help help_menu on_help mnemonic h help_menu tutorial labelString Tutorial help_menu tutorial mnemonic T help_menu tutorial sensitive False help_men
17. the invert toggle None of these operation actually modify the grey level image just how they are displayed The select overlay choice menu defines which overlay the colour and contrast controls will modify The colour sliders control the colour mixture for each domain and the contrast will modify the relative transparency of the wash overlay The buttons Save vtk and Save vff enable the colormap to be saved in a suitable format to be read into other programs in conjunction with the painted volume 6 USING A GRAPHICS TABLET 36 5 3 11 Autosave Dialog Autosave controls Autosave time sec OS eod Autosave save file tmp MAPaintAutosave 15999 Autosave recover file tmp MAPaintAutosave 15999 MAPaint occasionally crashes what a surprise To avoid losing too much work an autosave mechanism has been implemented which will save the entire painted volume at regular intervals This painted volume can then be read in and the domains extracted and assigned as required The original domain names are not currently restored so it is up to the user to be able to tell which is which In this version the restore mechanism is very slow so patience is required when recovering domains from the autosave file Each control is settable via an X11 resource By default the autosave directory is tmp which on Solaris is memory mapped therefore the autosave operation is usually very fast If the file has to be written to disk then
18. then error messages will appear on the command line when an attempt is made to use the tablet option 6 2 Generating Printed Views 6 3 Calibrating the Coordinate Mapping 7 Painting Techniques and Strategies 8 Conditions of Use The program MAPaint is provided in binary form freely for use by non profit institutions There is no charge for the use of the software and no guarantee The program is used entirely at the users own risk and the author and Medical Research Council can not be held responsible for any harm real or perceived arising from its use If versions are required for other Unix operating system versions or machine architectures please contact the author and source code can be provided for that purpose provided all new versions can similarly be made freely available 9 VERSION 38 9 Version MAPaint an X11 Motif program to interactively segment a 3D voxel image This program has been developed at the Medical Research Council UK Human Genetics Unit as part of the Mouse Atlas and Gene Expression Database project You are using version 1 0 For more information contact Author Richard Baldock MRC Human Genetics Unit Internet Richard Baldock hgu mrc ac uk Western General Hospital Phone 44 0 31 332 2471 Crewe Road FAX 44 0 31 343 2620 Edinburgh EH4 2XU UK
19. to ensure the file is saved if the machine has to rebooted set this to a directory not automati cally cleared autosaveFile MAPaintAutosave This file name will have the process id appended to generate a unique filename Note by default the au tosave file is removed when the program quits background grey85 XmScrollBar background grey95 fontList helvetica bold r 12 c XmText fontList 8x13 XmTextField fontList 8x13 XmList fontList 8x13 XmText background grey95 XmTextField background grey95 XmList background grey95 menubar XmCascadeButton marginWidth XmToggleButtonGadget selectColor red XmToggleButtonGadget visibleWhenOff True XmToggleButtonGadget indicatorSize 4 XmToggleButton selectColor red XmToggleButton visibleWhenOff True XmToggleButton indicatorSize 4 XmFrameWidget shadow Thickness 3 XmForm horizontalSpacing 4 XmForm verticalSpacing 4 XmFrame borderWidth 0 gamma 1 0 Colormap gamma value invert 0 Select inverted colormap numSolidOverlays 5 Number of solid overlay colours max 32 numWashOverlays 5 Number of wash overlay colours max 5 4 RUNNING MAPAINT 4 2 2 3D View 3D Section and OpenGL options Resource Default Comment work_area width 300 Width of the 3D feedback view work_area height 300 Heaight of the 3D feedback view work_area doublebuffer True OpenGL
20. Edinburgh Mouse Medical Research Atlas MRC Council Project Human Genetics Unit EMAP Technical Report MAPaint User Manual and Help Pages Author Richard Baldock Email R Baldock hgu mrc ac uk Date January 2001 Distribution Open distribution is permitted Status Draft Source Report 000013 MA Paint help Project DG401 Report number EMAP Report 000013 Keywords EMAP is a research programme at the MRC Human Genetics Unit in collaboration with Biomedical Sciences University of Edinburgh Contact Dr Duncan Davidson or Dr Richard Baldock at MRC Human Genetics Unit Crewe Road Edinburgh EH4 2XU UK Abstract This is a user manual and help pages combined for the program MAPaint which is for manual and image processing assisted segmentation of a 3D voxel image reference image into arbitrary 3d spatially non overlapping regions domains There is a more detailed document of the underlying program and geometry available in html or postscript The program has been developed as part of the Edinburgh Mouse Atlas and Gene Expression Database Project at the MRC Human Genetics unit in Edinburgh see http genex hgu mrc ac uk CONTENTS Contents Title Page 222coekoeebec bE A E 3X a x Ee nee Red ded x3 II A a i oe a e a aig a a a ea a e o 3 17 0 7 ca ee oe Ske LYE SER OEE a aaa A i e A e ee ke 1 Introduction 2 26 craneo scores RES RAR a EOS aoa Pe es 2 Basie Concepts and Terms 5 06 o es oe
21. RFACE button or key press Sequences of actions can be captured and replayed in order to make repeated sequences more efficient and to help the user avoid spending time and effort on a recordable repeat The macro menu buttons are Start record Start recording a sequence of actions all other buttons on this menu except End record will become inactive Only one macro can be recorded therefore pressing this will automatically delete the previous macro End record Stop recording the action sequence and make the menu buttons active Replay Replay the action sequence Loop Continous reply of the action sequence This makes all macro buttons except Quit loop inactive Quit loop Stop the continuous reply of the macro 5 2 8 Help Menu e hl Options Misc Help Paint Index On context On windows ESE On help Pueri Version The Help menu conforms to the Motif style pro viding help on context as well as a per window basis The Help system requires either that a Netscape browser is running on the X display or that it is possible to start up Netscape on the machine running MAPaint The help pages will be downloaded from the MRC as html therefore the machine must also be connected to the Inter net The help pages can be installed locally but help on context and on windows can not be supported without a WWW server 5 THE USER INTERFACE 5 3 Dialogs 5 3 1 Read Write Reference Dialogs E M
22. String nitial range morph_parameters labelString Morphological Operator Params morph_controls_form struct_elem labelString SE type morph controls form size labelString SE size affine options labelString Affine Transform Options 4 2 14 Domain Review Dialog Resource Default Comment review dialog popup mappedWhenManaged False review dialog dialogTitle review dialog src domain title labelString review_dialog domainSource labelString review_dialog domainSource review_domain labelString review_dialog domainSource mapaint_domain labelString review dialog domainSource read domain labelString review_dialog src_domain labelString review dialog domain review read labelString review_dialog dest_domain_title labelString review_dialog Discard labelString review_dialog Greys labelString review_dialog review_planes_title labelString review_dialog review_scan_control_title labelString review_dialog review_scale labelString review_dialog segment_domain labelString review_dialog segment_domain set review_dialog segment_planes labelString review dialog segment planes set read review obj dialog dialogTitle read review obj dialog pattern Domain Review Controls Source domain Source Review domain MAPaint domain Read domain MAPaint domain Read Destination domain Discard Greys Review planes Scan control Review scale Segment domain True Segment planes True Read Review Object w
23. a simple alternative to using the computer mouse and the benefit is that drawing with a pen is often more natural and easier to control for detailed positioning The user is still required to look at the screen to define the domain To use the system in this mode the sofware that comes with the tablet for the host machine is installed as per the instructions and no modifications are required in MAPaint in this mode so far as the program is concerned user events generated by the tablet are indistinguishable from that of the computer mouse In the second mode of use printed images of each section are generated and the user draws with the tablet pen or puck directly on the sheet The tablet coordinates generated by this action are then converted directly to voxel coordinates and thereby to define the domain For this mechanism the tablet coordinates are read directly by MAPaint and converted using the coordinate mapping defined by the tablet reference points set in the tool controls dialog The tool controls points are the coordinates in the reference image of two points that will be input from the tablet Typically these will correspond to some fiducial point printed with the image on the sheet but could also be fiducial markers embedded with the embryo and stained to be visible 6 1 Installing WACOM tablet MAPaint will automatically detect and initialise the tablet if it is switched on and connected to serial port A If it fails to find the tablet
24. ass through domains of higher dominance This will be changed in future versions This works on the assumption that the view can be segmented into a set of non overlapping domains These are defined as connected regions of any pre defined domains and connected regions of the remaining grey level image On selection pressing the left mouse button within the region the region will be filled with the currently selected domain colour if it has higher enough dominance If delete meta button or middle mouse button is required only regions of the current painting colour will be deleted irrespective of the dominance There are no settable parameters Erode Dilate Selecting clicking any domain with the left mouse button will dilate it selecting with middle mouse button or meta left button will erode it T his will apply to domains of any colour not just the current selection Erode and dilate are morphological operations which can be thought of as adding or subtracting all pixels with a certain distance of the existing edge The range and distance measure are settable parameters Affine An arbitrary affine transform translate rotate scale and shear can be applied to the selected domain any colour The current transform is selected by clicking the left 5 THE USER INTERFACE 23 mouse button with the control key pressed The transform is indicated by the cursor shape The tool controls allow which transforms can be selected note trans
25. at a time and each will appear in its own colour with a maximum of thirty two possible colours see Domain Menu In general the different do mains will have common boundaries and for convenience boolean rules are imposed on the domains determined by a dominance ordering such that domains of higher dominance will always win over domains of lower dominance The dominance ordering can be modified interactively using a drag and drop interface see Domain Controls It is also possible to set a mask from which all domains will be excluded see Domain Controls Individual colours and the grey level colour map can be redefined see Colomap Controls Defining arbitrary regions by hand is very time consuming and required intense concentration and so a number of power assist tools have been provided see Painting Tools These use image processing techniques to assist the manual segmentation process A reference document is available which provides a fuller description of the program and give the details of the view geometry and image processing and analysis functions in html or postscript 2 Basic Concepts and Terms The underlying assumption within paint is that the user wishes to define an arbitrary region or regions of 3D space within the space defined by a 3D voxel image termed the reference image These regions are termed domains and it is assumed that during any one session the domains to be defined do not overlap although they ma
26. e The purpose of this is to allow painting in planes which are otherwise not part of the reference image If min domain is also selected then paint will introduce a domain to an empty plane which is the union of the two adjacent non empty planes 5 THE USER INTERFACE 28 El Read 3D Object Filter ard MouseAtlas src MAPaint src wlz The choice menu below the directory and file windows alows the selection of other image formats Selecting a format will automati cally reset the filter for the default file exten sion If the required file does not have this ex Directories Files CE 9 00550 l MAPaintSectObj wlz tension then it can still be input but to make ae eee esis the file visible in the file list change the fil small wlz ter line to read in all files by removing the surface Wiz following the arterisk and pressing return or click the filter button See sec input data formats for a list of the available formats Woolz Ics Stanford Density Se Sunvision VFF BioRad Confocal Visualization Toolkit TK Il slc s srce MAPaint src4 The sec output data formats include the option of writing to a series of 2D image files 5 THE USER INTERFACE 5 8 2 Reference Properties Dialog Bounding box Planes 2 Lines y Columns x Object Properties 26 51 223 t 388 Voxel parameters Background 255 A 4 06 TA 4 00 IC
27. e section displayed is defined by the viewing parameters see the paint reference document The distance parameter is accessible directly via the slider on the view dialog and is defined as the perpendicular distance from the fixed point to the displayed section The slider range will be set to allow the display to pan through the whole 3D image When the distance is zero the fixed point is in the plane and will be visible if the fixed point display toggle has been set see fixed point menu below The controls toggle will make the section orientation controls visible which allows a number of modes of navigation through the 3D volume The basic mechanism for painting is the user selects a particular view for defining the domain Once that view is selected the window border will be inset and coloured red All controls to that window will be disabled and no other view can be selected until the painting operation in the 5 THE USER INTERFACE 32 selected view is complete Completion of a painting operation is usually done by pressing the right mouse button or The paint operation that will be invoked is the tool selected in the Options Paint Tools menu 5 3 6 Tools Controls Dialog 5 3 7 Domain Review Dialog Source domain Source MAPaint domain MAPaint domain domain 1 wiz Read Review planes ejejejeje e u njs u u sisi a ui Scan control Mi Segmentdomain Segmentplanes Review scale ma Discard IN
28. ed using Dynamic Programming and is an approximation to the snake cost making this optimisation globally correct is straightforward and will be implemented soon Once the domain has been tracked the tool provide the paint ball behavior to allow immediate editing and correction of the estimated new domain The parameter settings of the paint ball will be those last set when paint ball was selected or otherwise the defaults Settable parameters are sampling controls spacing and range which determine the number of sampling perpendiculars around the boundary and the search distance from the boundary snake cost parameters which determine the cost the new boundary is the minimum cost path of departing from the original boundary in terms of distance angle and curvature image cost parmeters which in this case is the size of the sampled image for comparison the cost is a normalised sum of the absolute grey level differences Edge Tracking Modify an existing domain using the same snake as in the image tracking but with the image cost determined by the absolute value of the image gradient high is low cost and the continuity of the edge direction so that edges of opposite polarity around the boundary are avoided The settable width parameter is the full width half maximum of the Gaussian function used to smooth the images when the gradient is calculated This can help to avoid high frequency noise arising from texture Tablet In many cases it
29. eters labelString Snake Cost Parameters image cost parameters labelString Image Cost Parameters edge tracking controls form nu dist labelString Distance edge tracking controls form nu alpha labelString Angle edge tracking controls form nu kappa labelString Curvature edge tracking controls form nu direction labelString Direction tablet ref points labelString Tablet Reference Points tablet controls form x1 labelString X1 tablet controls form y1 labelString Yl tablet controls form x2 labelString X2 tablet controls form y2 labelString Y2 paint draw params labelString Draw Paint Parameters paint draw controls form cursor labelString Cursor Type paint draw controls form paint shape labelString Paint Shape paint draw controls form paint border labelString aint Border paint draw controls form blob size labelString Paint size geometry params labelString 2D Geometry Parameters geometry controls form geom type labelString Object type geometry controls form object size labelString Object size geometry controls form fixed circle labelString Fixed circle geometry controls form fixed square labelString Fixed square geometry controls form variable circle labelString nteractive circle geometry controls form variable square labelString nteractive square threshold params labelString Threshold Parameters threshold controls form connect labelString Connectivity threshold_controls_form range label
30. f the user wishes to navigate by finding a point known to be in the required section this point can be set as the fixed point and then adjusting the viewing direction will result in planes passing through that fixed point A further navigation tool id provided by a second fixed point in which case the degrees of freedom are reduced to a single angle psi which defines rotation around the fixed line Given the viewing co ordinates there is still ambiguity about orientation of the displayed section on the screen Two options have been defined with only one currently available which are walking round the statue and up is up These are also detailed in the reference document 3 INSTALLING MAPAINT 3 3 Installing MAPaint MAPaint has been developed in C with the X11 Motif window system It will therefore only work with Unix systems There are earlier versions of the program which run on SGI but this version has only been tested on Solaris 2 5 or higher If versions are required for other architectures then please contact the author Source can be made available for compilation on other Unix systems 3 1 System Requirements Operating system Solaris 2 5 or higher CPU in principle any that can run Solaris 2 5 in practice a Sparc 10 or better is required for a reasonably interactive response The current development machine is a Sun Ultra 10 RAM for interactive sectioning the available RAM should be about double to volume of the 3D vo
31. h 0 4 2 12 View Dialog Resource Default Comment view_dialog save_section labelString Save view_dialog dismiss labelString Dismiss view_dialog help labelString Help view_dialog XmForm horizontalSpacing 4 view_dialog XmForm verticalSpacing 4 view_dialog XmFrame borderWidth 0 view_dialog scrolled_window borderWidth 3 view dialog section title form verticalSpacing 0 view dialog section title form borderWidth 0 view dialog section frame title labelString Section view dialog section frame FB toggle labelString filled 3D view view_dialog section_frame_FB_toggle highlight Thickness 0 view dialog section frame direction toggle labelString view direction view_dialog canvas borderWidth 0 view dialog distance slider labelString Distance view dialog controls frame title labelString Controls view dialog view scale labelString Scale view_dialog view_mode labelString View Mode view_dialog theta_slider labelString Yaw view_dialog phi_slider labelString Pitch view_dialog psi_slider labelString Line Rot view_dialog up_test labelString Up Vector view_dialog fixed_1 labelString Fixed Point view_dialog fixed_2 labelString Fixed Line view dialog up vector labelString Up Vector view dialog save settings labelString Save view dialog graphical fl labelString Point select view_dialog textual_fl labelString Type in coords view_dialog fiducial f1 labelString Select fiducial view_dialog display_fl labelString Display
32. ill always win over domains of lower dominance with the exception of when a domain is read in using the read domain menu option see Domain Menu In this case the domain read in is temporarily placed at the top of the dominance hierarchy To define or modify a domain the user selects a view window and then uses the painting tools to define the domain voxels The selected view window becomes highlighted and only one window can be used for painting If painting in a different view is required then the first view must be de selected by confirming that painting has finished in that window right button press As soon as painting in a window or plane finishes all other view windows will be updated if they have overlapping voxels Typical usage of the program is to define a domain in one plane then to move to the next parallel plane and define the voxels for the same domain In many cases these will have almost the same 2D distribution therefore paint has the facility to propagate the 2D domain defined in one planar section to the next Propagation is user controllable and will provide warning if requested if existing domains will be modified by the propagation process This process is supported by the auto increment option which if on will automatically move the view to the next plane when painting finishes see Domain Menu Each domain appears as a coloured region overlaid on the grey values of the reference image The first five colours appear a
33. includes the save and Save State restore the programs state and the define and run macro options Restore Selecting save state will popup a file selection dialog to allow the current state of the program to be saved to disc in the form of Start Record f an X Resources file These resources can be incorporated as part of a users XDefaults and therefore will be invoked as MAPaint starts Replay or can be read in using the Restore option with the result the interface will reconfigure to match the saved state In this version the Quit loop view dialog state is not saved and so this op tion is probably of little use The macro system is described below End record Loop 5 2 7 Macro Menu Macro Tear off The macro facility allows the user to record a sequence of actions which can then be re Start Record played so that series of repeated actions can 7 be automated On replay the actions involv End record ing interaction with the image e g one of the painting tools will wait until painting is con firmed before continuing Replay Loop Quit loop Hint always tear off this menu when recording a macro or when running a macro in Loop mode This avoids the menu popup actions being part of the macro and in some circumstances it is very difficult to quit from a loop if the menu is not already visible The macro facility records sequences of X11 Xt actions which result from user interaction e g a 5 THE USER INTE
34. is easier and more convenient to draw on printed pictures of the sections which can be done using a graphics tablet This is useable simply as a means to control the cursor the use of a pen to draw is more natural and easier to control than a mouse but the main use is to draw from the printed sections To link tablet coordinates with image coordinates the user defines two fixed points on the tablet which are transformed to two given points within image space The user first marks each point then draws around the required region The tool controls allow the THE USER INTERFACE 24 user to define the image coordinates of the reference points These points could of course match fiducial markers within the sectioned material if they exist The tablet controls are for a Wacom cordless tablet e PaintTools 3D There are currently no 3D painting tools In the next version 3D geometric objects 3D morphological operations and 3D threshold will be available e Tool Controls The tool controls dialog displays the settable parameters for the currently selected painting tool Parameters for each tool remain fixed from the last setting irrespective of the current selection See the sec tools controls dialog for details e Domain Review This will popup the domain review dialog to allow a controlled review of a domain input from disc Review in this sense means the presentation of the segmented parts of the domain with simple options to the colour de
35. late is always selectable and is the default The change in position and shape of the selected domain is indicated by the change in shape of the domain boundary which will take effect on button release Pressing the meta key when selecting a domain will select all visible regions of that colour for transformation i e select all Image Tracking Modify the domain propogated from the previous operation usually the previous section by using the image information associated with that domain to match to the existing image The method matches small parts of the image near to the domain and establishes the best match at a series of points along the domain boundary This is closely related to the snake techniques developed for flexible model matching but with a number of differences The first is that there is no global assumption about the image match cost the matching at each point on the boundary depends on the image used to define the initial boundary This breaks the requirement that the snake must have the same appearence at all parts The second is that there is no constraint on the absolute curvature of the boundary only a constraint on the change of curvature with respect to the original This allows the preservation of specific sharp features in the boundary which may be real There is a control panel which allows the modification of a set of control parameters for the searched area and the snake cost function The cost function is optimis
36. lz 4 RUNNING MAPAINT 4 2 15 Surgery Dialog 10 Resource Default Comment surgery_dialog_popup mapped When Managed False surgery_dialog dialogTitle Domain Surgery Controls surgery_dialog src_domain_title labelString Source domain surgery dialog src domain labelString MAPaint domain surgery_dialog surgery_option labelString Surgery option surgery_dialog dest_domain_title labelString Destination domain surgery_dialog Discard labelString Discard surgery_dialog Greys labelString Greys 4 2 16 Colormap Dialog Resource Default Comment colormap dialog popup mappedWhenManaged False colormap dialog dialogTitle Colormap controls colormap dialog form borderWidth 0 colormap dialog overlay borderWidth 0 colormap dialog overlay labelString Select overlay colormap dialog gamma labelString Gamma colormap dialog low_thresh labelString Low colormap dialog high thresh labelString High colormap dialog red labelString Red colormap dialog green labelString Green colormap dialog blue labelString Blue colormap dialog contrast labelString Contrast 4 2 17 Autosave Dialog Resource Default Comment autosave dialog popup mappedWhenManaged False autosave_dialog dialogTitle autosave_dialog autosave_time labelString autosave_dialog autosave_file labelString autosave_dialog autosave_recover_file labelString autosave domains dialog dialogTitle A
37. main to be moved with the middle mouse button and drop it on the required location The domains in the range from the starting position to the drop position will be rotated either up or down in dominance according to the the direction of the drag The result will be an adjustment of the dominance hierarchy The Cancel button dismisses the controls dialog There should be a reset button to be done e Auto increment Pressing the auto increment toggle will enable the auto increment action after painting the plane As soon as painting in a plane is completed right button press or return key after the last painting action then that view will increment by a distance of one unit and will switch immediately into paint mode This will continue until either the auto increment action is switched off by pressing the toggle again or the end of the 3D image is reached e Propagate If propagation is enabled by pressing the propagate toggle then the starting paint domain in a particular view will be the union of the existing domain in that view and the previously painted domain This is of most use in conjunction with auto increment and means that for each plane the starting paint domain is the correct domain from the adjacent parallel plane In many cases this will only require minor modification and therefore will be quicker than re painting the entire domain If the propagated domain is going to modify an existing domain of the same colour on that
38. nd a region which is then filled or by brushing These incorporate Domain surgery jThreshold both append and delete modes Ge hi ometry Object and Tablet provide two other primary input modes the Colormap Erode Dilate other options all modify or use existing m domains Domain review Geometry object Auto segment Fill Autosave Affine Image Tracking Edge Tracking Tablet Details of the settable control parameters for each tool are given in the paint tools controls section The tools follow a fairly consistent behavior e g left button adds paint whereas middle button or meta left button removes paint The currently selected paint tool is in dicated by the appearance of the paint tool toggle button which will appear depressed and have a red in the indicator If one of the views has been selected for painting then the cursor in that view window may also have been changed to indicate which tool is selected Actions common to all 2D painting tools when the cursor is in the painting view and painting is selected are Right arrow next section increase distance by 1 Left arrow previous section decrease distance by 1 Up arrow next paint tool above on the tool menu list Down arrow next paint tool below on the tool menu list lt meta gt Up arrow select next domain above on the domain menu list meta Down arrow select next domain below on the domain menu list Right bu
39. ns not all tissues have pre defined domains however every voxel does have an associated tissue If the tissue domain button is selected then the corresponding domain will be read in and appended with the currently selected painting domain see sect 5 2 3 Reading from the anatomy menu also provokes the 3D display of the current domain In future versions of the program any component will be selectable with the response that the program will generate the required domain from the given pre defined domains In some cases this will involve the union of multiple domains and in others the domain read in will include the requested region and possibly more 5 THE USER INTERFACE 5 2 3 Domain Menu C TIONEM File Anatomy Domain View Options Misc Help Select Controls Auto increment Propogate Read domain Write domain Clear domain Display 3D domain Clear all domains Write painted volume ree e Select The domain menu allows selection of the cur rent domain controls for the dominance or dering controls for the painting behavior do main I O clear and 3D display The full painted volume can also be saved for use in other 3D display systems e g VTK Each option is discussed in more detail below The domain menu has a tear off to allow per manent placement of the menu on the screen for convenience This is a pull right cascade menu which al Select
40. nt mnemonic A domain_menu auto_increment borderwidth 0 domain_menu propogate labelString Propogate domain menu propogate mnemonic P domain_menu propogate borderwidth 0 domain_menu read_domain labelString Read domain domain_menu read_domain mnemonic R domain_menu write_domain labelString Write domain domain_menu write_domain mnemonic WwW domain menu save domain labelString Save domain domain menu save domain mnemonic a domain_menu three domain menu three domain menu write domain menu write domain menu select domain menu clear domain labelString domain menu clear domain mnemonic domain menu clear a l domains labelString display domain labelString _display_domain mnemonic paint volume labelString paint volume mnemonic orderWidth Clear domain n all domains Display 3D domain Wie painted volume 0 4 RUNNING MAPAINT 4 2 6 View Menu Resource Default Comment view_menu labelString View view_menu mnemonic V view_menu borderWidth 0 view_menu x_y_view labelString X Y view view_menu x_y_view nemonic X view_menu y_z_view labelString Y Z view view_menu y_z_view nemonic Y view_menu z_x_view labelString Z X view view_menu z_x_view nemonic Z view_menu arbitrary view labelString Arbitrary view_menu arbitrary_view nemonic A 4 2 7 Options Menu Resource Default Comment options menu labelString Options options menu mnemonic O option
41. ow the user to select specific planes to review The process of review will automatically loop through all planes and all parts within a plane and when all parts within a plane are assigned the button for that plane becomes insensitive Scan control Set the Segment domain toggle on if the domain on each plane should be segmented into unconnected regions for independent allocation Set the Segment planes toggle on if the planes of the input domain should considered independently this toggle has no action in version 1 0 When domains are being reviewed the controls of the section view used for review are insensitive use the Review scale choice menu to adjust the display scale Destination domain When review is in progress the region to be assigned is flashed on the section view The user can then choose to which domain the flashing region should be appended by pressing the corresponding button in the Destination domain area Discard means that the flashing region will ignored and any domains within that region left unchanged Greys means that the flashing region will be set to Grey thereby clearing any parts of any domain within the region Note assignments respect the dominance hierarchy If no assignment is possible but it is required that the region is kept for further review then press the Stop button or select a different plane by pressing the corresponding button Action buttons e Review Start the review process This will loop through
42. pe and paint brush eraser size and whether the cursor includes a white border for clarity Geometry object Define the domain by placing a geometric object at the cursor location when the button is pressed T his can be useful for spotting objects for the purposes of location or counting rather than detailed delineation Control parameters are the object shape and size Threshold When a pixel is selected by pressing left or middle mouse button a domain is Fill defined by thresholding the image in a range defined by the grey value at the selected pixel and the range parameter This region will comprise all pixels connected to the initial pixel which have value within the range and for which all pixels within the con nection path are also within the threshold range the image is threshold above and below to retain all pixels that lie in the range this image is then segmented and the region which includes the selected pixel is selected On button press the region to be painted will display and if the cursor is dragged right or left the threshold range will increase or decrease respectively This will have the effect of increasing and decreasing the area of the modified domain respectively Settable control parameters are the segmentation connectivity 4 or 8 neighbour and the initial range parameter Currently the tool ignores other domains for the purposes of region selection which gives the unexpected result that the region seems to p
43. plane then the user is prompted to check if this is required before continuing Yes will result in the union of the propagation domain and the existing domain No will leave the existing domain unchanged Selecting No does not switch propagation off except for this plane e Read Domain Read in a domain object to the currently selected painting domain A file selection dialog is popped up and the default action is to form the union between the new object and the existing painted regions Modifying this default will be possible when the control panel is implemented See Read Write Domain Dialogs for more details e Write Domain Write out the currently selected domain as a 3D object A file selection dialog will be popped up to allow the user to easily define the image file Once saved using Write Domain the 5 THE USER INTERFACE 19 filename used will become the default for this domain See sec read write domains dialogs for more details e Clear Domain Clear the current domain this could lose a lot of work if used carelessly and therefore the user is asked to confirm the action WARNING Until an undo action is implemented once cleared there is no way of restoring the lost domain e Clear All Domains Clears all domains Quicker than clearing one at a time but more dangerous This action erases any memory of defined domains not saved to disc and there is no undo or cancel action The user is given one chance to quit the option
44. s wash overlays through which the grey values can be seen The remaining colours 27 are solid but when deleted or temporarily lifted will reveal the underlying reference image The number of colours is by default 10 but this can be modified by setting an X11 resource Practice has shown that the wash colours are the most useful because keeping the reference image visible makes editing easier but there is a limitation to 5 because the paint program has been designed to work on an 8 bit display The colour of each overlay the intensity of the wash and the grey level look up table of the reference image can all be adjusted interactively see Colormap Dialog Paint allows the domain voxels to be defined within any arbitrary section view of the reference image This view is defined by a set of viewing coordinates which comprise a fixed point 3D a viewing direction and a distance The section through the reference image is perpendicular to the viewing direction and at the given distance from the fixed point These co ordinates and transformations are defined in the reference document The viewing direction is defined by two angles phi and theta which can be thought of as pitch and yaw respectively If these angles are kept constant then adjusting distance will display parallel planes from the reference image Initially the fixed point is set at 3D co ordinate 0 0 0 but this can be reset at any time Rotation is always about the fixed point therefore i
45. s_menu borderWidth options menu paint tools 2D labelString options menu paint tools 3D labelString options menu tool controls labelString options_menu tool_controls mnemonic options menu domain review labelString options_menu domain_review mnemonic options menu domain surgery labelString options_menu domain_surgery mnemonic options_menu auto_segment labelString options_menu auto_segment mnemonic 0 Paint tools 2D Paint tools 3D Tool controls Domain review D Domain surgery S Auto segment A options menu colormap labelString Colormap options menu colormap mnemonic C options menu autosave opts labelString Autosave options_menu autosave_opts mnemonic A 4 2 8 Miscellaneous Menu Resource Default Comment misc menu labelString Misc misc_menu mnemonic M misc_menu macro labelString Macro misc_menu macro start_record labelString Start Record misc_menu macro start_record mnemonic S misc_menu macro end_record labelString End record misc_menu macro end_record mnemonic E misc_menu macro replay labelString Replay misc_menu macro replay mnemonic R misc_menu macro loop labelString Loop misc_menu macro loop mnemonic L misc_menu macro quit_loop labelString Quit loop misc_menu macro quit_loop mnemonic Q misc_menu save_restore labelString Save Restore misc_menu save state labelString Save State misc_menu restore_state labelString Restore misc_menu save_restore
46. save_state labelString Save State misc_menu save_restore restore_state labelString Restore 4 RUNNING MAPAINT 4 2 9 Help Menu read obj dialog dialogTitle read obj dialog pattern read obj dialog file type labelString Read 3D Object wlz Select image type write obj dialog write obj dialog write obj dialog write obj dialog object props dia object props dia object props dia object props dia object props dia object props dia object props dia object props dia object props dia object props dia object props dia object props dia object props dia object props dia object props dia object_props_dia XmFileSelection XmFileSelection XmFileSelection XmFileSelection XmFileSelection XmFileSelection XmFileSelection save state dialog read obj dialog file type borderWidth write_obj dialog popup mappedWhenManaged dialogTitle pattern file type labelString file_type borderWidth og_popup mapped When Managed og dialogTitle og control horizontalSpacing og control verticalSpacing og framel titlel labelString og form1 planes labelString og form1 lines labelString og form1 kols labelString og form1 planes_vals labelString og form1 lines_vals labelString og form1 kols_vals labelString og frame2 title2 labelString og form2 background labelString og form2 x size labelString og form2 y_size labelString og form2 z
47. sed com mands in this version of MA Paint this is just a reset button for the 3D display The Anatomy menu see section 5 2 2 be comes sensitive if the reference image has been read in from the Edinburgh Mouse Atlas CD ROM using the Theiler stage option of the File menu In this case a highly simplified 3D outline of the embryo is displayed yellow lines in the figure The Help menu see section 5 2 8 will access these help pages provided the help page URL resources are set correctly Netscape browser is available and if the host computer is con nected to the Internet 13 5 THE USER INTERFACE 14 5 1 1 3D Display 4 I MA Paint ts 14 4j The 3D feedback window is fully interactive File Anatomy Domain View Options Misc Help and allows the user to modify the view of the 3D scene by rotation scaling and translation The interaction model for rotation is that the scene is embedded in a sphere which the user can rotate by clicking the left mouse button in the scene and dragging If no views are selected for painting then the 3D view will move If the mouse button is released while the mouse is still in motion then the 3D view will continue to move as if thrown Drag ging the left mouse button up down with the shift key pressed results in a re scaling of the scene and dragging the middle mouse button will translate the scene The reset button will return the viewing co ordinates and scale to the default val
48. stination of each part See the sec domain review dialog for details e Domain Surgery Domain surgery allows the cutting of existing domains into two parts by defining a cutting surface Currently the only cutting surface option is the plane defined by a given view In the next version a laser cut will be included See the sec domain surgery dialog for details e Auto segment Not yet implemented See the sec autosegment dialog for details e Colormap The display colormap can be controlled by adjusting the visible grey level ranges and the gamma value Each domain colour can be also be adjusted as well as the relative contrast of colour to grey value wash overlays only See the sec colormap dialog for details e Autosave Like any large program paint is not bug free therefore an autosave option has been included which saves all of the painted domains at predetermined intervals which defaults to 15 minutes This time is user settable and autosave can be switched off but is not recommended Data can be retrieved from an old autosave file and the user is presented with the domains from the saved file and prompted to assign the domains as required See the sec autosave dialog for details 5 THE USER INTERFACE 25 5 2 6 Misc Menu M M M da dal The Miscellaneous menu is the catch all for View Options Misc Help facilities common to all Mouse Atlas Motif in terfaces Currently this
49. t result in a further menu are indicated by an arrow to the right 5 THE USER INTERFACE 15 of the label buttons that result in a dialog window are indicated by following the text 5 2 1 File Menu I MA Paint ts 14 21 ul l The file menu provides for read and write of File Anatomy Domain View Options Wisc Help the reference image The write option is pro New vided to allow conversion to another image format and to allow image property changes e g voxel size background value to be saved Write reference to disk The properties are viewed and mod Ref properties ified by selecting the Properties button from the menu The Theiler Stage button allows selection Theiler setup of a Theiler stage reference image and pre defined anatomy from the Mouse Atlas CD ROM The root of the CD ROM is defined via the Theiler setup option or via an X11 resource Open reference Theiler stage 5 2 2 Anatomy Menu EE TONNES File Anatomy Domain View Options Misc Help embryo gt branchial arch extraembryonic component Mere branchial groove and arch cavities and their linings ectoderm limb mesenchyme notochord organ system pie sre IL adem toman endoderm tail bud a branchial_membrane 3rd_arch a branchial_pouch mandibular_component maxillary_component maxillary mandibular groove
50. the process may take a number of seconds depending on the size of the reference image The autosave filename will by default have the process ID appended in order to generate an unique filename The button controls are On switch the autosave mechanism on Off switch the autosave off Recover recover domains from the given Autosave recover file It is usually worth switching autosave off for this action and in general any existing domains should have been saved If the process runs out of memory during this action the program will usually quit Dismiss popdown the Autosave dialog Help probably does nothing 6 Using a Graphics Tablet MAPaint is designed and intended for use as a tool to define arbitrary regions within the 3D space defined by a grey level voxel image The painting actions are all undertaken using the screen pointing device which is typically a mouse or trackball For drawing accurately this can be difficult and many users find it more natural to use a pen like device for drawing The simplets device for 7 PAINTING TECHNIQUES AND STRATEGIES 37 this is a graphics tablet and therefore the possibility of using a tablet has been included For this purpose support for the WACOM UltraPad tablet has been programmed in specifically with code for the cordless pen and 4 button puck The tablet can be used in two ways The first is an alternative input to control the screen cursor In this mode the pen or puck can be used as
51. tton confirm quit painting in this view This will result in the domains of this view being installed and provoking all views to update and redisplay The 3D feedback view will be released In all cases except confirm the view will remain in painting mode If the section has been changed then the domains from the prior section will be committed and marked as changed In brief the 2D paint tools are as follows Draw Use the cursor by default a dot but settable to an arrow or sights to define a closed boundary as an arbitrary combination of rubber band straight line links or free hand curves On confirm right button or return key the start and end of the curve will be 5 THE USER INTERFACE 22 joined by a straight line the enclosed region filled and then used either to append to the existing domain set union or to subtrat from the existing domain set difference If the drawing started with the meta key shown with a diamond sign on Sun workstations pressed or if the drawing was done with the middle mouse button then the drawn domain will be subtracted from the existing domain of that colour The cursor type is the only settable parameter Paint ball Use the cursor by default circular settable to be a square to paint in or erase an area Painting will respect the dominance hierarchy erase will only erase from the domain of the selected colour whatever the dominance Settable control parameters are the paint brush eraser sha
52. u version labelString Version help menu version mnemonic V 4 2 10 File Dialogs Resource Default Comment read_obj_dialog_popup mapped When Managed False 4 RUNNING MAPAINT 4 2 11 Domain Dialogs Resource Default Comment domain_controls_dialog_popup mapped When Managed False domain_controls_dialog dialogTitle Domain controls domain controls dialog dominance labelString Domain Dominance domain controls dialog control horizontalSpacing 5 domain controls dialog control verticalSpacing 5 domain controls dialog dominance frame borderWidth 0 domain controls dialog dominance form borderWidth 0 domain controls dialog domain 1 labelString 1 domain controls dialog domain 2 labelString 2 domain controls dialog domain 3 labelString 3 domain controls dialog domain 4 labelString 4 domain controls dialog domain 5 labelString 5 read domain dialog popup mappedWhenManaged False read domain dialog dialogTitle Read 3D Domain read domain dialog pattern wlz write domain dialog popup mappedWhenManaged False write domain dialog dialogTitle Write 3D Domain write domain dialog pattern wlz write_paint_volume_dialog_popup mapped When Managed False write_paint_volume_dialog dialogTitle Write 3D Painted Volume write_paint_volume dialog pattern wlz write paint volume dialog file type labelString Select image type write paint volume dialog file type borderWidt
53. ues nd When a view window is opened the outline of the window will be displayed in the 3D scene and will move as the viewing parameters are modified By this means the viewing window can be positioned relative to the displayed 3D domains A view window that has been selected for painting will be highlighted in red This will also temporarily switch off the 3D interaction until painting has been completed The 3D view of domains is toggled on and off using the Display 3D domain option on the Domain Menu When the 3D view is set into motion the display will update after a certain period ms If the displayed domains are very complex this period may be shorter than the time required to recalculate the display In this situation it is possible for the 3D feedback processing to hog all the available processing and interaction with the program becomes very slow If this becomes a problem it is important to ensure that the 3D view is stationary Only when a view is selected for painting are the 3D view updates paused 5 2 Pull down Menus Some of the pull down menus from the menu bar can be pinned i e made permanently visible on the screen This is for convenience for commonly used actions menus that can be pinned have a dotted line tear off at the top of menu pop up The menu windows can be removed from display by double clicking the top left close button of the menu window Within each menu buttons tha
54. utosave controls utosave time sec utosave save file utosave recover file Autosave recover domains 4 3 Input Data Formats User images can be read into MAPaint to define the reference image to define painted domains and as a domain to be reviewed The reference and painted domains must be 3D data 2D images can be read in for review but must be mapped directly onto a section through the reference image Permitted input formats are 4 RUNNING MAPAINT 11 Name File extension Source woolz wlz Woolz is the native im age format for MA Paint http genex hgu mrc ac uk Software woolz ICS ics ids Standard for Image Cytom etry Data Files Cytometry 11 1990 561 569 Stanford Density den http white stanford edu Sunvision vff 3D voxel format for Sunvision now incorporated as part of AVS Ex press BioRad Confocal pic 3D format for the BioRad confocal microscope VTK vtk Native format for the Visualisation Toolkit http www cs rpi edu martink SLC slc If other image formats are required then use e g netpdm tools or the program convert from ImageMagick 4 4 Output Data Formats MAPaint allows image data to be output from the file menu domain menu and the view dialog These can be in 3D or 2D format with an enumerated sequence of 2D image if required Output formats are 5 THE USER INTERFACE 12 Name File extension Source woolz wiz Woolz is the native im
55. view_dialog graphical f2 labelString Point define view_dialog textual_f2 labelString Type in coords view_dialog fiducial_f2 labelString Select fiducials view_dialog display_f2 labelString Display view_dialog graphical_uv labelString Point define view_dialog textual_uv labelString Type in coords view_dialog fiducial_uv labelString Select fiducials view_dialog display_uv labelString Display 4 RUNNING MAPAINT 4 2 13 Tool Controls Dialog Resource Default Comment tool_control_dialog dialogTitle Painting Tool Controls tool control dialog XmForm borderWidth 0 tracking controls form XmFrame borderWidth 0 tracking parameters labelString Tracking Parameters tracking controls form spacing labelString Spacing tracking controls form range labelString Range tracking controls form size labelString Size snake cost parameters labelString Snake Cost Parameters image_cost_parameters labelString mage Cost Parameters tracking_controls_form nu_dist labelString Distance tracking controls form nu alpha labelString Angle tracking controls form nu kappa labelString Curvature edge tracking controls form XmFrame borderWidth 0 tracking parameters labelString Tracking Parameters edge tracking controls form spacing labelString Spacing edge tracking controls form range labelString Range edge tracking controls form size labelString Width snake cost param
56. xel image For the 9 day mouse embryo approx 10MBytes on a Sun workstation 64MBytes is sufficient the window system occupies about half Disk space The binary occupies about 2 2MBytes In normal operation the autosave option requires space equal to the size of the input grey level voxel image The autosave feature can be switched off Software environment MAPaint requires an X11R5 or higher X Window server either with OpenGL extensions or with the Mesa OpenGL dynamic libraries MAPaint will also use the Sun XIL extensions if presents and installed 3 2 Obtaining the Program Contact the author or from the WWW site http genex hgu mrc ac uk where it is available for download as a compressed tar file 3 3 Installation The tar file should be uncompressed and unpacked in some suitable place e g opt MouseAtlas MA Paint The binary can then be copied as required e g to opt MouseAtlas bin with users executable path appropriately modified If the Mesa software implementation of OpenGL is required then this can be obtained from the Mouse Atlas site or directly from http ssec wisc edu brianp Mesa html 4 Running MAPaint MAPaint is simply run from the command line usually in the directory containing the reference voxel image or where the painted domains are to be stored MAPaint can also be set up to run from window manager menu but the user will then be required to switch to the desired directory MAPaint does not use any user
57. y have a common boundary It also assumed that the spatial resolution of the reference image defines the resolution of the domains i e the domain boundaries are defined by the voxel boundaries of the reference image In paint version 1 0 the reference image must be a grey level image and the native image format is woolz This means that the image is not restricted to a rectangular array of voxel values but to a set of values defined within an arbitrary region of 3D space The only restriction on the domains is that they can only be defined within this 3D region i e the user is not allowed to paint on regions not in the reference image As each domain is painted this modifies an internal record of the painted voxels but does not modify the reference image Domains and the reference image are independent 3D image structures defined which map into the same co ordinate frame but which can be independently read written and modified To save a defined domain it is necessary to select it and then write to disc Attempting to quit paint with modified but unsaved domains will result in a warning message which if ignored 2 BASIC CONCEPTS AND TERMS 2 will result in a loss of the domain when the program quits The saved domains are woolz binary domain objects which can be externally modified by the various woolz filters and programs Within paint the domains are ordered in a dominance hierarchy The effect of dominance is that domains of higher dominance w
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