PHASEQUANT (User Manual)
Contents
1. containing just one segment gt Bring up the Phase Measurement frame by clicking Phase Measurement button in the toolbar gt Select a mask containing two segments in the top drop down box and select a mask containing one segment in the bottom drop down box PhaseQuant User Manual 9 gt Select Inter Phase Distribution utility and click Process button at the bottom gt After processing a new mask called Inter Phase is created in the ROI pane This mask will contain the segment from the second mask with the gray values replaced with the enclosing segments in the first mask Video Demo http www youtube com watch v SzcscgdAT8k 5 GROUND TRUTH OPTIMIZATION 5 1 Ground truth validation The masks generated in PhaseQuant can be validated against Ground Truth GT data to measuring the margin of error gt Open the ground truth image gt Click on the relevant mask in the ROT pane to make it visible Ground Truth l ound Truth Image 0449_GT tif Register Mask Data 0 255 128 Process Fig 5 Ground truth optimisation module gt Click Ground Truth Optimization button from the Toolbar and this will bring up a new window named Ground Truth Now select the GT image from the drop down box below Ground Truth Image label and select the mask from the drop down box below Mask Image label Specify the slice number of the mask f2. phase segmentation frame by clicking Phase Extraction button in the toolbar PhaseQuant User Manual 7 gt Select Add Results to the Log File check box gt Now results of the segmentation will be written to the log file Video Demo http www youtube com watch v dPBAxbQeuKO 4 PHASE MEASUREMENT MODULE 4 1 Modal abundance gt Bring up the Phase Measure frame by clicking Phase Measurement button in the toolbar gt Select the region or mask Phase Measurement from the drop down box Select Phase gt Select Modal abundance e in satel Mla ean option and click Process Objectisize distribution 2D button at the bottom Object size distribution 3D Loads Object Counter3D Plugin gt Results are displayed in a Porosity new window with volume Inter Phase Distribution fraction in percentage and Metal x number of pixels voxels in Process Cancel square brackets Fig 4 Phase measurement module Video Demo http www youtube com watch v no9yUqveeil 4 2 Object size distribution 2D amp 3D PhaseQuant User Manual gt Bring up the Phase Measurement frame by clicking Phase Measurement button in the toolbar gt Select the mask from the drop down box gt Select Object size distribution 2D option and click Process button at the bottom gt After processing PhaseQuant generates a shape mask representing each object with a unique color and also displ
3. the bottom drop down box if there is an overlap PhaseQuant User Manual 6 Note Calculator and CalculatorPlus utilities in ImageJ can be used to combine the masks if there is no overlap between the masks but while using those utilities the user has to make sure that the masks to be combined are visible in respective image windows and also to uncheck the Create new window check box Video Demo http www youtube com watch v no9yUqveeil 3 5 Reduce border Often it might be necessary to reduce the outer border of the specimen to remove spurious pixels that result due to partial volume averaging process gt Bring up the Phase Extraction frame by clicking Phase Extraction button in the toolbar gt Select a mask from the drop down box which needs border reduction gt Select Reduce border utility and specify the number of pixel layers to be stripped off in No of Layers textbox gt Click Process button at the bottom of the Phase Extraction frame to start the reduction Note Border reduction can only be performed on a mask and cannot be performed on a region Video Demo http www youtube com watch v 4bI 1 Wpso048 3 6 Log file The results of the segmentation can be written to a log file which is a text file gt Create a new text file anywhere on the computer gt Click Log File Location button in the toolbar and browse to the location of the text file created in the previous step and click open gt Bring up the
4. PHASEQUANT User Manual NHM PhaseQuant gt Ground Truth IA Update J Log File ae Phase 2 Phase 4 Optimization A Histogram Location W Segmentation Measurements Q Region of Interest a EJ CT data ROI Pane Toolbar cf Regionimask C Silicates O Metal C Silicate mask Threshold Bar gt MN Threshold Display CJ Training data C DensityiPhase D Phase 1 0 gt avg pixel 4 Phase 2 0 gt avg pixel 1 Training Pane Buttons J Collective Histogram a Segment Histogram 4 Calibrate Histogram 9 Apply Temporary Calibration Apply Permanent Calibration Fig 1 PhaseQuant GUI 1 INSTALLATION AND LOADING 1 1 Installing PhaseQuant gt Download the zip file from the following link http imagejdocu tudor lu doku php id plugin segmentation phasequant_ start gt Unzip the contents to the ImageJ plugins folder gt Restart ImageJ gt PhaseQuant can be found in NHM folder under plugins menu PhaseQuant User Manual 1 Note PhaseQuant will also install Object_Counter3D plug in from http rsb info nih gov ij plugins track objects3 html Video Demo http www youtube com watch v RF5HVUwDHaY 1 2 Loading PhaseQuant gt Open an image or stack gt Load PhaseQuant Note PhaseQuant will not load without an active image or stack in ImageJ Video Demo http www youtube com watch v ZdUDa1 PPc0g amp feature related AllendeIn
5. Resin0501 tif 50 10 44 10 98 mm 924x97 2 16 bit 1 7MB Segment 3 Segment 1 Segment 2 Fig 2 Regions masks and segments 2 BASIC UTILITIES 2 1 Combined Running histogram gt On clicking Collective Histogram button PhaseQuant will update the canvas with histogram of the entire stack PhaseQuant User Manual 2 gt On clicking Running Histogram button PhaseQuant will update the canvas with histogram of the current slice and will continue to refresh the canvas as the current displayed slice is changed in the stack window Video Demo http www youtube com watch v 9WDfj9EvDXM amp feature related 2 2 Update histogram gt Existing utilities in ImageJ such as smoothing and sharpening filters can be applied to the image stack while PhaseQuant is in operation gt Changes made by external utilities can be registered to PhaseQuant by clicking Update Histogram button in the toolbar Video Demo http www youtube com watch v dB XIBbSJrAs amp feature related 2 3 Manual segmentation This utility is used for segmenting the stack or image into multiple regions based on thresholds gt Click Segment Histogram button and subsequently Threshold Bars will shown up on the histogram in the canvas gt Dragging the Threshold Bars will change the upper and lower thresholds and the corresponding region in the stack image is highlighted with a unique colour map The threshold values will be displayed in the T
6. ays a result window with size distribution statistics object identifier phase ID size of the object in voxels pixels Note On clicking Object size distribution 3D PhaseQuant loads an existing plug in named Object Counter3D This plugin is well documented and further information about this plug in can be found in the following link http pacific mpi cbg de wiki index php 3D_Objects_Counter If you are using Object size distribution 3D in PhaseQuant it is imperative to cite the reference provided in the above link Object size distribution 2D option does not require a binary mask whereas Object size distribution 3D requires a binary mask Video Demo http www youtube com watch v PA YmY OY Pr6c 4 3 Porosity gt Create a region by thresholding the bulk everything except air and porosity of the specimen using manual segmentation gt Bring up the Phase Measurement frame by clicking Phase Measurement button in the toolbar gt Select the bulk from the drop down box gt Select Porosity option and click Process button at the bottom gt After processing a new mask called Porosity is created with segmented void spaces and shows up in the ROI pane Video Demo http www youtube com watch v un4LyOOOS V4 4 4 Inter Phase Distribution Inter Phase distribution utility can be used for measuring distribution of a segment within other segments This option requires two inputs one containing two segments and another
7. be com watch v pQqiSZIUTU 6 DENSITY CALIBRATION MODULE This is a module for calibrating micro CT image stack for density so that the stack can be standardised Recording Density Phase 6 1 Recording density data gt To record training data click Add Data button at the bottom of the Training pane which will bring up a new frame gt Select the check box next to the Density label in the new frame and now start selecting the Record pixel values in the image stack window Once PhaseQuant User Manual 11 completed assign a density value to the data set gt Click Record button to register the density data set and this will show up in the Training pane gt Repeat the procedure to register more density data sets Video Demo http www youtube com watch v M_UgoSOHpF0O NHM PhaseQuant j gt Ground Truth Update J Log File Phase 2 Phase Optimization Histogram Location Segmentation Measurements io Region of Interest EA CT data C Regionmask 12528 J DensityiPhase B Density 1 2 gms ce av Ly Density 2 2 gmsice av O Density 2 8 gms ce avi Density 7 6 gmsice avi J Collective Histogram i i Segment Histogram 6 Calibrate Histogram 9Y Apply Temporary Calibration Apply Permanent Calibration Fig 7 PhaseQuant GUI while density calibration 6 2 Density calibration gt On clicking Calibrate Histo
8. egmentation Five segmentation methods are included in PhaseQuant two of the methods require training sequences and others don t require training data All the segmentation methods split the regions into two segments and create a new mask gt Bring up the Phase Extraction frame by clicking Phase Extraction button in the toolbar gt Select one of the regions created by manual segmentation from the drop down box gt Choose the phase segmentation method to be used for segmentation gt If the selected segmentation method requires training sets indicated by TS required in the phase extraction window then select Use Training Data check box at the bottom and chose the training data sets from the drop down boxes below gt Click Process button at the bottom of the phase segmentation frame to start segmentation PhaseQuant User Manual 4 gt Once segmentation is complete a new mask titled New Mask is created and shows up in the ROI pane gt Onclicking the mask a new window opens with the segmented image Note It is important not to close the windows as it might crash the program On clicking the top level node region named Region mask in the ROI pane all the windows except the main window will disappear Video Demos http www youtube com watch v nISIOJYnIAY http www youtube com watch v no9yUqveeil Phase Extraction SEE Select Phase 3 2 Cluster analysis hd Cluster analysis utility lets a user specify
9. gram button PhaseQuant will display density vs gray value plot in the canvas gt On clicking Apply Temporary Calibration button PhaseQuant applies calibration to the current slice and displays the calibrated image in a separate window PhaseQuant User Manual 12 gt On clicking Apply Permanent Calibration button PhaseQuant applies calibration to all the slices and updates the histogram Video Demo http www youtube com watch v M_UgoSOHpF0 PhaseQuant User Manual 13
10. h the image data Video Demo http www youtube com watch v nISIOJYnIAY 3 3 Convert to mask A manually segmented region can be converted into a binary mask using this utility gt Bring up the Phase Extraction frame by clicking Phase Extraction button in the toolbar gt Select a region from the drop down box which needs to be converted into a binary mask gt Select Convert to mask utility and click Process button at the bottom of the Phase Extraction frame to start the conversion Video Demo http www youtube com watch v no9yUqveeil 3 4 Combing masks The masks created by different segmentation methods can be combined together It is often difficult to precisely segment the images manually and as a result there is an overlap between successive regions While combining masks generated by processing the regions using the Calculator and CalculatorPlus utilities in ImageJ it often results in an overlap as the manual segmentation may not have been precise and margins might overlap This problem has been addressed with Combine mask utility gt Bring up the Phase Extraction frame by clicking Phase Extraction button in the toolbar gt Select Combine mask utility and select the masks to combine in the two drop down boxes below and click Process button gt Anew mask will be created in ROI pane with the masks combined together gt The mask selected at the top drop down box takes precedence over the mask selected at
11. hreshold Display textbox in the Region of Interest ROI pane gt Anew region can be added to the PhaseQuant by pressing the Add Region button at the bottom of the ROI pane gt The new region will show up as ROI pane titled New Segment and can be renamed by clicking on the region or deleted by clicking Delete Region button Video Demo http www youtube com watch v stR VcCFTDMs amp feature related 2 4 Recording training sequence PhaseQuant User Manual 3 gt Some segmentation methods included in PhaseQuant require training data for processing gt To record training data click Add Data button at the bottom of the Training pane which will bring up a new frame gt Select the check box next to the label phase in the new frame and start selecting the pixel values in the image stack window Once completed assign a label to the data set for identification this must be a number gt Click Record button to register the training set and the training set will show up in the Training pane The training sets can be renamed or deleted as per user s convenience gt Repeat the procedure to register more training sets Note On clicking Error button at the bottom of the Training pane PhaseQuant will bring up a frame with statistical information mean and variance on the training datasets Video Demo http www youtube com watch v YHbSfyZHWcc amp feature related 3 PHASE EXTRACTION MODULE 3 1 Automatic s
12. or which GT corresponds to in the textbox right next to Slice no label Now list all the gray values taken by segments in the mask in the textboxes below Mask Data label and list corresponding gray value in the GT image under GT Data label On clicking Process button at the bottom the segments in the mask is compared against segments in the GT image and an Error Image visualising the discrepancy between actual and software measurements is generated along with the information on the margin of error in percentages for each segment in a separate window PhaseQuant User Manual 10 Video Demo http www youtube com watch v k9ZgCyqC4q4 5 2 Importing training data Training datasets can be generated automatically from the GT data using this utility gt gt Open the ground truth image Click on relevant mask in the ROI pane to make it visible Click Ground Truth Optimization button from the Toolbar and this will bring up a new window name Ground Truth Now select the GT image from the drop down box below Ground Truth Image label and select the mask from the drop down box below Mask Image label Specify the slice number of the mask for which GT corresponds to in the textbox right next to Slice no label On clicking Register button in the center PhaseQuant registers the pixel values corresponding to each segment in the GT image into training data sets and lists them in Training pane Video Demo http www youtu
13. the minimum i 3 Kmeans clustering and maximum bounds on the cluster size of each Parzen windows TS required i segment in a mask O Windowing NN C aa Er gt Bring up the Phase Extraction frame by Windowing NN TS required clicking Phase Extraction button in the toolbar Reduce border gt Select a mask from the drop down box on o of Layers E which cluster analysis is to be performed Convert to mask gt Specify the gray value of the segment to be 2 Combine mask metalmask m processed in Seg textbox and minimum size of Sad hori k the cluster in Vol textbox and gray value to a oee replace with in Dat textbox if the cluster is R eg 28 Vot 40 Dat 255 smaller than the value specified in Vol Preview gt Click Preview button to process current slice Add Results to the Log File and preview the results Don t Use Training Data B on gt Click Process button in the bottom of the _ Use Training Data raining Data for Phase 1 Phase Extraction frame to apply cluster Phase 1 0 gt avg pixel 6162 0 analysis to the entire stack permanently raining Data for Phase 2 Phase 2 0 gt avg pixel 19226 0 a Fig 3 Phase extraction 5 module Note Cluster analysis can only be performed on a mask and cannot be performed on a region After performing cluster analysis it might be necessary to hide the mask and reopen to refres
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