User Manual
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1. Cell Lenght V 2 0 User Manual Any comment or request please contact Dr Arturo Pimentel jarturo ibt unam mx Dr Gabriel Corkidi corkidi ibt unam mx Web page http www ibt unam mx labimage Download link http www ibt unam mx labimage proyectos arabidopsis 1 System requirements Java JRE Download java http www java com en download PC with Linux Windows or MAC OS 2 Abstract This software is designed to acquire data of the cell s length within different lanes over a collection of 2D images of roots The procedure enables the serial processing of images from the collection The traced lengths and coordinates from segments of the root within different lanes are stored and ordered in a text file which can be exported to any other statistical package By using this application acquisition time is largely reduced than if using simply ImageJ and stored data are ranged logically for further analysis 3 Instructions 1 To execute the graphic interface Figure 1 give a click to the executable file Cell_Length_V2 xx jar Press the button Define images folder 1 to locate the folder containing the images collection select the folder not a file within Once selected the information will appear in the notification window 13 At this point define the pixel size for calibrating the image collection in micrometers by using the window 2 After the images folder is selected this application explores the2. defined directory and builds up the list of images to be analyzed contained in the images folder Color or gray level images are accepted It also accepts different size of images and formats within jpg tif png gif The final list will be displayed in the notification window 13 At this point the button Start process 3 will be enabled and once activated the first image of the list will be displayed and its name will appear in window 11 This is the active image being analyzed 10 11 12 The wheel of the mouse can be used to zoom in or zoom out while displaying any image First point once over the center of the region to be zoomed Prior beginning to take measures press the button Start measurements 5 This will enable the active image to receive the measuring clicks Point the cells borders defining sequentially their lengths to be measured Figure 2 A complete lane of cells can be traced During the measuring process defined before any point can be deleted by using the button Delete last point 6 and continue tracing the correct point The image selector 12 can be used at any moment to select another image to for example compare adjacent cells when they are not well defined or out of focus in the active image When all cells lengths are marked the button End measurement 7 should be pressed The program will ask if the user needs to trace more measurements in the actual image for
3. example to repeat several times a lane to take a mean value or to trace different lanes or if he desires to change to the following image of the list Within an active image the user may perform multiples measures in different cell lanes over the same image If one of the measured lanes needs to be erased select the number of the lane to be erased with 9 and then press the button Delete measurement Data coming from erased lane will be excluded in the output file If all the lanes need to be erased from the file activate Delete all 10 Area 11 shows the active image under analysis When the sequence of images of the list is processed the button End process 4 should be pressed The measured lengths with additional data see Fig 3 will be saved in a simple text file with extension txt and it will be located in the same directory where the root images were stored when selecting directory with button 1 Figure 3 shows an example of file containing the name of the analyzed image the actual date the calibration pixel size then five columns showing the dataset label traced point label its corresponding x y coordinates in the image and the length of each cell The End process button 4 is always active and the program may be quitted at any moment and the active data will be saved in the text file The notification window 13 is designed to follow every step of the measuring procedure executed by the
4. image and a single one in the second image Note that the first length measured is within the second row Point 2 corresponding to the distance between points 1 and 2
5. program Root s dimensions measurement Images Analysis Laboratory IBt UNAM Define images folder pm Pixel 4 End process 2 3 Start process 5 6 7 Start measurement Delete last point End measurement Delete measurement n lt Delete all Analyzing image Showing 11 C IZ _ Figure 1 Graphical user interfase designed to measure the cells lengths into the images of the selected roots Figure 2 Image of a slice of Arabidopsis thaliana Nomarski microscopy showing the marked point in yellow to define the cells borders for measuring their lengths Image File agl1 2Col0 18 01 jpg Date 2015 01 26 12 11 45 Pixel size um pixel 1 0 Dataset Pointnumber Coordinate X pix Coordinate Y pix Distance um 0 1 464 480 0 2 487 478 23 0867928 0 3 508 477 21 023796 0 4 528 475 20 0997512 0 5 544 476 16 0312195 1 2 463 624 1 3 480 627 17 2626765 1 4 490 627 10 0 1 5 505 628 15 0332964 1 6 517 628 12 0 Image File agl12Col0 18 m 40x23 20x1 1 jpg Date 2015 01 26 12 11 45 Pixel size um pixel 1 0 Dataset Point number Coordinate X pix Coordinate Y pix Distance um 0 1 847 795 0 2 899 798 52 0864666 0 3 948 798 49 0 0 4 997 802 49 1629942 0 5 1048 804 51 0392006 0 6 1090 801 42 1070065 0 7 1138 798 48 0936586 Figure 3 Example of the output file dat once imported over MS Excel Two lanes were pointed in the first
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