Introduction to IKOSA AI

Improve your knowledge of the application training process with IKOSA AI.

IKOSA AI helps you develop custom microscopy image analysis applications without any coding or AI knowledge. To help you achieve this we have prepared a simple guide for you to go through the individual app training steps.

What to expect from this page?

App training preparation


Select images on your computer

You can train your applications on 2D or multichannel images.

Important: You cannot train your app on time series images.

Semantic Segmentation

Instance Segmentation

Semantic Segmentation

Instance Segmentation




standard and WSI

RGB and grayscale


standard and WSI

RGB and grayscale

8bit and 16bit

standard and WSI


8bit and 16bit

max. 10 channels

Important: Make sure your image file formats are supported by IKOSA Portal File formats

Important: Non-WSI formats of 2D and multichannel images are supported up to a maximum image size of 625 megapixels (e.g. 25,000 x 25,000 Pixel).


Login to IKOSA


Prepare your project

How to create a project?

How to upload images?


Project preparation rules

  • Use data with a high diversity of feature appearances.

  • Larger datasets provide better training results. However, small and medium datasets will work just fine if you prepare your images correctly.

  • The greater complexity of your data requires more images.


Prepare your images

How to annotate an image?

How to draw an ROI?

How to draw ROI(s) for application training with IKOSA AI?


Image preparation rules

Label set

Create a label set including at least 1 label (e.g. for a specific cell, tissue, or staining type)


Labeling, annotation and regions of interests

Use fully annotated and labeled images or ROIs to train your app.





If you use images for application training, fully annotate at least 2 images. It means that you should annotate and label ALL features. In total, you should have at least 100 annotations per label.

If you use ROIs for application training, you need to have fully annotated at least 1 ROI per image. It means that you should annotate and label ALL features inside and on the border of ROIs. In total, you should have at least 100 annotations per label.

A mix of images and ROIs

If you annotate some images entirely while using ROIs on others, in step 6, ensure to select the option to train your application on ROIs. This way, if an image doesn’t have any ROIs, the system will use the whole image.


Annotate ALL features

Features that are present but not annotated or labeled introduce counterfactual information into the trained application and impair the results (red arrows on the screenshot).


Don’t use point annotations

Semantic and instance segmentation applications require closed geometry type annotations (black arrows on the screenshot) i.e.

  1. rectangle annotations

  2. polygon annotations

  3. circle annotations , and freeform annotations .

Point annotations are NOT supported (red arrows on the screenshot) by IKOSA AI segmentation apps, because a point size equals 1 pixel, which isn’t enough for the app to learn and segment an area correctly.


Avoid overlapping ROIs

If some ROIs overlap and share the same annotations, these annotations will be counted for each ROI separately. Thus, in the training results, you will have a higher number of annotations in total, which originates from this overlap counted several times.

Moreover, the training will run through such “multiplied” annotations more often than the other ones, effectively giving them a higher importance in the training process.


Background recognition

The background of an image is an area that DOESN’T CONTAIN the features required for the app training. You add them to help the app differentiate between background and features to recognize, especially when they are very similar.

Background images/ROIs can be added at step 6 of the training process.



The IKOSA AI wizard Step-by-step

Go to the IKOSA AI section.


1. Read the introduction

Before starting a new training, learn all about IKOSA AI here in this article. The link from the IKOSA AI Introduction leads you to this page.


2. Select project

Select the project you have just prepared by annotating and labeling the data.


3. Select training type

Currently, IKOSA AI covers semantic and instance segmentation tasks only.


4. Select labels

Select labels relevant to the training.


5. Select dataset split

Training images are used to train the app, while validation images are used to assess its performance.

Random dataset split

Manual dataset split

Random dataset split

Manual dataset split

You select all images to be used in app development, and IKOSA randomly and automatically divides them into training (80% of the images) and validation datasets (20% of the images).

Select at least 1 training and 1 validation image.


The quality of training and validation images plays a crucial role in achieving high app performance. Your expert opinion, as demonstrated in tasks such as annotations, holds particular significance during the validation process. Your input makes a difference in the app training process.



6. Select images

  1. Choose between 2D and multichannel image type (only for instance segmentation)


  1. Select whole images or images with ROIs.


  1. Add background images/ROIs (optional)

You can use entire background images or images containing only background ROIs to enhance background recognition.

If you use images with specifically designated ROIs:

  • Select the “Performing the training on ROIs” option in the “Improve background recognition” section.

  • Choose your images.


7. Select training duration

Quick training is suitable for the initial app setup, while extended training is ideal for refining the app.


8. Review your selections and start the training

  1. Review your selections before starting your application training.

  2. Give your training a name and start it!


Wait until the training is completed

Overview of the results

As soon as the training is completed, you will receive a notification email. Then you can view your results directly in the IKOSA or download them.

Your results contain:

  • the report as a PDF file with quantitative outcomes and highest/lowest performance results as validation visualizations.

  • qualitative performance results as validation visualizations

  • confidence heatmap visualizations.


Go to the Training Evaluation section to quickly review your trained app performance or compare it with another one from a different training iteration for the same use case.


Are you satisfied with the training results?

Are you satisfied with the training results?




Share this information with your team members/colleagues and discuss your next training. Enjoy app training!

If you still have questions regarding your application training, feel free to send us an email at Copy-paste your training ID in the subject line of your email.

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