Cilika-External Docs

• Work Flow
• Introduction
• Getting Started
• Report
• Settings

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

The Cilika application is located on the home screen of your IOS. Locate the Cilika iOS application icon (green 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

Add Folder

1. Tap on the Add folder icon in the top-right (folder with a + sign) 
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.

Figure 1.2 (A) Add Folder

Figure 1.2 (B) Name Folder

Figure 1.2 (C) Save

Rename and Delete Folder

Long press the folder to get the following two options:

• Delete
• Rename

1. Once you tap on the Rename option, Rename Folder popup appears on the screen.
2. Enter a valid folder name with no space in between.
3. Tap on Save to save the new name or Cancel to get the previously saved name.
4. Tapping on the delete option deletes the whole folder, which includes any or all the files inside the folder.

Add File 

1. Tap the Camera icon 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.
5. If you are facing any more issues go through the troubleshooting guide.

2. Navigating Live Microscopic View

1.4 Understanding the Camera

Figure 1.4 Screen Layout

Live View — Screen Layout:
	Tools
1	Back (‹)	Tapping on the Back (‹) Chevron brings you back to the dashboard.
2
3	Crosshair / Reticle	This tool shows/hides the center target on your live view screen
4	Lock	locks the screen against accidental touches.
5	Settings (gear)	Opens Camera Settings.
6	Zoom Slider	Use ▲ / ▼ arrows to zoom in and out of the live Microscopic View fine adjustment.
7	Open Drawer	Opens a drop-down of annotation tools.
8	Scale Bar
9	Objective Lens	Helps

Zoom Slider

Location : Left Side

1. Locate the Zoom slider on the left side of the screen.
2. Find two arrows on either sides of the zoom bar.
3. Use the ▲ / ▼ arrows to zoom in or out of the microscopic image.
4. Drag up to zoom in on the microscopic image and Drag down to zoom out. The range of the zoom is between 1.00x to 5.00x.

Scale bar

Location : Bottom Left

how an why

Recording

Location : Bottom Center

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. Tap on the mic button to enable or disable the background sound.
   

3. Annotation and Measurement 

Open Tab - Undo/Redo

Location : Center Right

1. You will find an element labeled Open on your right.
2. Tap the Open drawer
3. A drop-down appears.
4. The Drop-down contains all the tools for markings, annotations and shapes.
5. Any annotations or measurements drawn can be undone, redone and deleted here as well.

Activation Cursor  

The activation cursor is the first icon in the drawer. This tool activates and deactivates the the annotation tools on the live view screen. 

Teaching Pointer

1. A Teaching Pointer is a digital cursor on the screen.
2. Can be used to highlight specific cells or areas during live demonstrations or training.
3. By default, only 1 Teaching Pointer appears on the screen.
4. Up to 4 Teaching Pointers can be used together at any given point.

Freehand

1. This tool helps create a freehand annotation like drawings or text.
2. Long-press or double tap the tool to open the Line Width, adjust line width.
3. If you wish to change the colour of the annotation
4. Tap on the red dot (●) in the drop down and change it to your desired color.

Line/Arrow

1. The line / arrow tool helps mark areas with distance is a circular shape.
2. Tap on the  O icon to create a circle. 1.2.
3. The size of the circle can be adjusted by dragging out the cursors. 1.3.
4. Tap on the icon again to adjust the line width, lock the shape or set the radius.
5. Tap Set to?? 1.4.
6. Once the shape is locked, pointer size can be adjusted accordingly.

Text

Circle

1. The circle annotation helps mark areas with distance in a circular shape.
2. Tapping on the O icon creates a circular shape on the live view microscopic screen.
3. The size of the circle can be adjusted by dragging out the cursors.
4. Tapping on the icon again brings out a popup where you can adjust the line width, set the radius manually and lock the shape.
5. You can adjust the line width by sliding the on the line width slider.
6. Once the shape is locked, pointer size can be adjusted accordingly.

Box

1. Tap on the □ icon in the Open drawer to create a box.
2. You can adjust the size of the box by moving the two cursors placed on either of the ends.
3. Another way to set height and width is by taping on the icon again.
4. The height and width can be set by typing in the measurements according to your preference.
5. Tap Set to here you can adjust the line width as well as lock the shape.

Dotted Marker

1. Tap on the S icon to get a dotted marker, this tool helps draw a dotted annotation/space.
2. Tapping on it again lets you adjust the line width.

Enclosed Shape

By tapping on the icon below the S icon, the tool will automatically connect your endpoint to your starting point with a straight line.

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	↷	Locate below the Undo option, it reverses the Undo command, reapplying the changes you just removed.
Erase		Scroll down and locate the erase Icon in the tools drawer. 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

Create Report

Figure 1

Following are the steps to "Create a Report" -

Once you tap on the the icon at the top right corner, 

1. Tap the Create Folder icon (folder with a + sign).

2. An Add Case dialog appears. Tap on the the dropdown button.

3. 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.

4.  If the folder does not appear, swipe down on the grid to refresh.

Figure 1.2	Figure 1.3
Figure 1.4	Figure 1.5

Generate Report 

1. 1. The new folder appears on the Report Page.
   Tap on the icon located at the extreme right (folder with a + sign)
2. Add in details to generate your report (Figure 1.5).
3. At the top center is located the "Report Name" titled as "Untitled". Tap on the same to change the name of your Report.
   Tap on "Generate" to generate the report. (Figure 1.8)

Report Settings

1. The settings option has two features, the Header and the Footer for the report. 

2. Tap on the right of the heading subsection (e.g. Name) to add in the designated details. 

3. The details typed in the subsection will be shown at the top in the Preview column.

4. These details will be added in the final report as Header and Footer.

5. Once the Header and Footer details are added in tap on Save to save the details.

Figure 2.7 Header
Figure 2.8 (A)Footer	Figure 2.9 (A)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.