Work Flow

Introduction
Cilika is a professional digital microscopy application developed exclusively for iPad to support organizational and laboratory workflows requiring rigorous specimen documentation and analysis. The application integrates image capture, annotation, dimensional measurement, calibration, and report generation into a single platform suitable for pathology laboratories, clinical environments, research facilities, and educational institutions. 
 Quick-start steps 
 
 
 Set up: install Cilika on iPad, connect microscope camera, check system requirements. 
 
 
 Calibrate: run the calibration routine once per objective or setup to ensure measurement accuracy. 
 
 
 Capture image: open Capture, choose objective and illumination, focus, then tap Capture. 
 
 
 Annotate: open image, use drawing/text tools to mark features and add notes. 
 
 
 Measure: select measurement tool (line, area, scale-linked), measure features; verify units. 
 
 
 Save & organize: tag images, add metadata (sample ID, date, operator), and save to project. 
 
 
 Export & report: generate a PDF or image package with embedded measurements and annotations; share via secure export or institutional storage. 
 
 
 Troubleshoot: refer to the FAQ for common issues (connection, focus, calibration). 
 
 
  

Getting Started
  
 Navigating Cilika 
 
   
   
 The Cilika application is located on the home screen of your IOS. Locate the Cilika iOS application icon ( ) in the dock at the bottom of the screen and tap on it to launch the Cilika application.  
 
 The dashboard has three icons at the top right corner: 
 
 
 Add Folder 
 
 
 Generate Report 
 
 
 Settings 
 
 
 1. Add Folder 
 1. Tap on the  Add folder icon in the top-right ( )  
 2. An  Add Folder dialog appears. 
 3. Type in a clear, unique name (for example the case number or patient identifier) is to be                 added in the text box.  
 4. Tap  Save, for the new folder to appear on the Dashboard. 
 
 
 
 
 
 
 
 
 
 
 
 
 
   
 2. Rename and Delete Folder 
 1. Long press the folder to get the following t wo options: 
 
 
 Delete ( ) 
 
 
 Rename ( ) 
 
 
 2. Once you tap on the Rename ( ) option,  Rename Folder popup appears on the screen. 
 3. Enter a valid folder name with no space in between. 
 4. Tap on Save to save the new name or Cancel to get the previously saved name. 
 5. Tapping on the Delete ( ) option it deletes the whole folder, which includes all the files               inside the folder. 
 
 
 
 
 
 
 
 
 3. Capture Image 
 1. Tap the Camera ( ) located on the folder beside the folder name. 
 2. A camera opens up, this is the Live Microscopic View . 
 3. Make sure the iPad is horizontally positioned for it to work. 
 4. If the microscopic image is not visible on screen, restart the application. 
 
 
 
 
 
 
   
 
 
 
 
 
 
 
 
 
 
 
 4. Navigating Live  Microscopic View 
 
 
 
 
 Understanding the Camera 
 
 
 
 
 
 
 Figure 1.4  Screen Layout 
 
 
 
 
 
 
 
 
 
 (A) Live View — Screen Layout:  
 
 
 
 
 
 
 
 Tools 
 
 
 Description 
 
 
 
 
 1 
 
 
 Back (‹) 
 
 
 Select the Back (‹) arrow to return to the folder. 
 
 
 
 
 2 
 
 
 Measurement (M) 
 
 
 Show or hide the exact measurements of selected areas and annotations on the slide. 
 
 
 
 
 3 
 
 
 Crosshair / Reticle ( ) 
 
 
 Shows or hides the center target in the live microscopic view. 
 
 
 
 
 4 
 
 
 Lock ( ) 
 
 
 Locks the screen to prevent accidental touches during viewing or capture. 
 
 
 
 
 5 
 
 
 Settings ( ) 
 
 
 Opens Camera Settings. 
 
 
 
 
 6 
 
 
 Zoom Slider 
 
 
 Use the ▲ / ▼ arrows to zoom in or out and make fine adjustments to the live microscopic view 
 
 
 
 
 7 
 
 
 Open Drawer 
 
 
 Opens the annotation tools available for marking the live microscopic view. 
 
 
 
 
 8 
 
 
 Scale Bar 
 
 
 Displays the scale of the image to help estimate the size of the viewed specimen or region. 
 
 
 
 
 9 
 
 
 Objective Lens 
 
 
 Displays the currently selected objective lens or magnification level.   
 
 
 
 
 
 
 Zoom Slider 
 1. The Zoom Slider is located on the left side of the screen. 
 2. Drag the slider  up to zoom in on the live microscopic image or down to zoom out. 
 3. Use the ▲ / ▼ arrows to make fine zoom adjustments. 
 4. The available zoom range is  1.00x to 5.00x . 
 
 
 Scale Bar 
 1. The Scale Bar displays the measurement scale of the microscopic image, for example, 30.0           µm. 
 2. Check the  Objective Lens displayed in the bottom-right corner, such as 4x, 10x, 40x, or 100x . 
 3. Ensure that the selected  Objective Lens matches the magnification of the microscope to             maintain accurate image scaling and measurements. 
 
 (B) Recording 
 1. Find a Capture and Recording button.  
 2. Tap on the  Circle Button ( ) located at the bottom center of the screen. 
 3. To switch to video, you can tap on the  Video Button ( ) to the left. 
 4. You can also add a  reference image ( ) to the screen if it has already been configured in the        Main Settings . 
 4. Tap on the Mic button ( ) to enable or disable the background sound. 
 5. After capturing the live view, enter a valid  File Name in the Details dialog box, then select             Save to save the captured image. 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 5. Annotation and Measurement 
   
 5.1 Open Drawer : 
 1. Locate the  Open Drawer on the right side of the screen. 
 2. Select the  Open Drawer to display the drop-down menu. 
 
 
 
 
 
 
 
 
 
 
 (A) Steps for the Annotation Tools 
 
 
 
 
 
 Tools 
 
 
 Purpose 
 
 
 Steps 
 
 
 
 
 Activation Cursor ( )  
 
 
 
 Enables or disables the annotation and marking tools on the live microscopic view. 
 
 
 
 
 Select the  Activation Cursor ( ) in the Open Drawer . 
 
 
 Use the annotation tools when enabled. 
 
 
 
 
 
 
 Teaching Pointer ( ) 
 
 
 Highlights specific cells, structures, or areas on the live microscopic view for teaching, demonstrations, and discussions. 
 
 
 
 
 Select the Teaching Pointer ( ) . 
 
 
 Place the pointer on the required area. 
 
 
 Press and drag to reposition it. 
 
 
 Use up to four Teaching Pointers simultaneously. 
 
 
 Configure the number of pointers in General Settings ( ) . 
 
 
 
 
 
 
 Freehand ( ) 
 
 
 Draws freehand annotations on the microscopic image. 
 
 
 
 
 Select the Pencil icon ( ) from the annotation tools in the Open Drawer . 
 
 
 Use your finger or stylus to draw the required annotation directly on the image. 
 
 
 Long-press or double-tap the Freehand tool to open the Line Width settings and adjust the thickness of the annotation. 
 
 
 To change the annotation color , select the red dot ( ) in the drawer and choose the required color. 
 
 
 
 
 
 
 Line\Arrow ( ) 
 
 
 Draws a straight line or arrow to indicate a specific region or measure a distance. 
 
 
 
 
 Select the Line/Arrow icon ( ) to place a line on the microscopic image. 
 
 
 Select the tool again to adjust the line width . 
 
 
 Drag the handles at either end of the line to adjust its length and position. 
 
 
 The measurement displayed near the line indicates the distance represented by the line. Drag the line to reposition it as required. 
 
 
 To hide the measurement, select the M icon to turn the measurement display off. 
 
 
 
 
 
 
 Text ( ) 
 
 
 Adds labels, notes, or other text directly to the microscopic image. 
 
 
 
 
 Select the Text (A) icon to open the Custom Text dialog box. 
 
 
 Enter the required label or note in the text field. 
 
 
 Select Set to place the text annotation on the viewing area. 
 
 
 Position the text at the required location on the image. 
 
 
 
 
 
 
 Circle (O) 
 
 
 Highlights a specific region using a circular annotation. 
 
 
 
 
 Select the Circle icon (O) to create a circle on the image. 
 
 
 Drag the available handles to adjust the size of the circle. 
 
 
 Select the Circle tool again to access additional options, such as Line Width, Lock, and Radius . 
 
 
 Enter the required radius, if applicable, and select Set to apply the value. 
 
 
 Once the circle is locked, adjust the pointer size as required. 
 
 
 
 
 
 
 Box ( ) 
 
 
 Highlights a rectangular region of interest. 
 
 
 
 
 Select the Box icon ( ) to create a rectangular annotation. 
 
 
 Drag the available handles to adjust the height and width of the box. 
 
 
 Select the Box tool again to enter specific Height and Width values . 
 
 
 Enter the required measurements and select Set to apply them. 
 
 
 Use the available options to adjust the Line Width or lock the shape in place. 
 
 
 
 
 
 
 Dotted Marker ( ) 
 
 
 Marks a specific area using a series of dots. 
 
 
 
 
 Select the S icon ( ) to activate the Dotted Marker tool. 
 
 
 Place the dotted marker on the required region of the microscopic image. 
 
 
 Select the tool again to adjust the Line Width , if required. 
 
 
 
 
 
 
 Enclosed Shape ( ) 
 
 
 Creates a closed annotation by automatically connecting the endpoint to the starting point. 
 
 
 
 
 Select the Enclosed Shape icon    ( ) in the Open Drawer. 
 
 
 Draw the required shape around the region of interest. 
 
 
 When you finish drawing, the tool automatically connects the endpoint to the starting point with a straight line, creating a closed shape. 
 
 
 Adjust the shape or its properties using the available annotation controls, if required. 
 
 
 
 
 
 
 Rendering ( ) 
 
 
 
 Rendering permanently applies annotations and markings to the current image so that they are included when the image is saved or exported. 
 
 
 
 
 Scroll through the tools in the  Open Drawer and locate the Rendering icon ( ). 
 
 
 Select the  Rendering icon to apply and save the current annotations and markings to the image. 
 
 
 After rendering, the annotations and markings appear as part of the saved or exported image. 
 
 
 
 
 
 
 Annotation Color 
 
 
 The annotation color can be customized to make different annotations easier to identify and distinguish on the slide. 
 
 
 
 
 In the Open Drawer on the right side of the screen. 
 
 
 Select the red dot ( ) color indicator in the drawer. 
 
 
 A color selection menu appears with available options such as Grid, Spectrum, and Sliders for selecting a color. 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 (B) Error Recovery Tools 
 
 
 
 
 Tools 
 
 
 Symbols 
 
 
 Features 
 
 
 
 
 Undo 
 
 
 
 
 
 This reverses your last performed action or a series of action and is located at the very top of the open drawer. 
 
 
 
 
 Redo 
 
 
 
 
 
 It reverses the Undo command, reapplying the changes you just removed. 
 
 
 
 
 Erase 
 
 
 
 
 
 
 
 This tool Erases only unwanted annotations. 
 
 
 Tapping on it again, lets you adjust the wide of the eraser. Adjust it depending on how much area you want to erase.  
 
 
 
 
 
 
 Delete All 
 
 
 
 
 
 Instantly clears all current annotations, markings, and measurements from the live view or image.

Report
10. Report 
 Following are the steps to " Create a Report " - 
 Once you tap on the the report icon at the top right corner,  
 
 
 Figure 10 
 
 Tap the  Create Folder icon in the top-right (folder with a + sign). 
 An  Add Case dialog appears. Tap on the the dropdown button. 
 The dropdown gives a list of all the folders saved or created on the dashboard. Select the folder you wanna add and tap Save  ( Figure 2.4 ) .  The selected folder appears on the screen. 
 If the folder does not appear, swipe down on the grid to refresh. 
 
 
 
 
 
 
 Figure 10.1 
 
 
 
 Figure 10.2 
 
 
 
 
 
 Figure 10.3 
 
 
 
 Figure 10.4 
 
 
 
 
 
 Generate Report  
 
 The new folder appears on the Report Page. Tap on the icon located at the extreme right  
 (folder with a + sign) to add in details to generate your report ( Figure 1.5 ). 
 At the top center is located the "Report Name" titled as "Untitled". Tap on the same to change the name of your Report. 
 Once the details and slides are added in tap on " Generate",  on the top right corner to generate the report. ( Figure 1.8 ) 
 
 
 
 
 
 
 Figure 10.5 
 
 
 
 Figure 10.5 
   
 
 
 
 
 
 Figure 10.5 
 
 
 
 Figure 10.5 
 
 
 
 
 
 Report Settings 
 
 The settings option has two features, the  Header and the Footer for the report. 
 Tap on the right of the heading subsection (e.g. Name ) to add in the designated details.  
 The details typed in the subsection will be shown at the top in the  Preview column. 
 These details will be added in the final report as  Header and Footer. 
 Once the  Header and Footer details are added in tap on Save to save the details. 
 
 
 
 
 
 
 Figure 10.6 Header 
   
 
 
 
 
 
 Figure 10.7 Footer 
 
 
 
 Figure 10.8 Footer

Settings
Live View Settings 
 App Settings 
 
 
 
 
 
 
 
 Exposure & ISO: 
 Use Exposure Duration (shutter speed) and ISO together to control image brightness and motion. Short/fast exposures (e.g., 1/1000 s) freeze motion and darken the image; long/slow exposures (e.g., 2 s) brighten it but may cause blur. Raise ISO to brighten low-light shots at the cost of more noise; lower ISO for cleaner images in good light. 
 Focus & Zoom: 
 Enable Focus to manually refine magnification and achieve precise sharpness on live view. Use Hide Zoom Slider to remove the on-screen zoom control when you want a cleaner interface or to prevent accidental zoom changes.