🔍 Introduction and Goal 

The Cell Behavior Video Classification Challenge (CBVCC) is a challenge designed to develop/adapt computer vision methods for classifying videos capturing cell behavior through Intravital Microscopy (IVM).

IVM is a powerful imaging technique that allows for non-invasive visualization of biological processes in living animals. Platforms such as two-photon microscopes exploit multiple low-energy photons to deliver high-resolution, three-dimensional videos depicting tissues and cells deep within the body. IVM has been used to visualize a wide range of biological processes, including immune responses, cancer development, and neurovascular function. 

The primary goal of the CBVCC challenge is to create models that can accurately classify videos based on the movement patterns of cells. Specifically, the models should be able of:

  • Identifying videos where cells exhibit sudden changes in their direction of movement.
  • Distinguishing these from videos where cells show consistent, linear movement, stationary cells as well as from videos containing only background.

The CBVCC challenge aims to provide a platform for researchers to develop innovative methods for classifying IVM videos, potentially leading to new insights into biological processes.

 

👩‍🔬👨‍🔬 The CBVCC Challenge 

The CBVCC challenge will be open to researchers from all over the world. Participants will be asked to develop computational models to classify IVM videos. The models will be evaluated based on their accuracy to classify videos.

The challenge will be divided into two phases:

  • Phase 1: In the first phase, participants will be provided with a training dataset and a test dataset of IVM images and labels. They will use this data to develop and evaluate their models.
  • Phase 2: In the second phase, participants will submit their results obtained on a distinct test dataset of IVM images. The models will be ranked based on their performance on the test dataset.

The challenge results will be decided based on the performance of the Phase 2 submission. 

 

🏅 The Challenge timeline

The CBVCC challenge will begin on September 15th, 2024, and end on December 20th, 2024. The timeline of the key events is organized as follows:

  • September 15th 2024 to November 15th 2024: Participants are invited to join the challenge by registering on the website.
    Registration link: https://forms.gle/cQSHJmEFZ5bRBJ328
  • November 15th 2024: The train dataset will be published, officially launching the challenge. Additionally, a validation leaderboard will be made available for participants. 
  • December 6th 2024: Test dataset (not annotated) released.
  • December 20th 2024: Challenge closes. By this date participants are required to submit their predictions on the test set, an abstract describing the methodology, code or docker container to replicate results.
  • January 7th 2024: Results and winners will be announced.

Dataset 

The CBVCC dataset consists of 2D video-patches extracted from IVM videos. These videos capture the behavior of regulatory T cells in the abdominal flank skin of mice undergoing a contact sensitivity response to the sensitizing hapten, oxazolone. The videos are acquired either 24 or 48 hours after the initial skin challenge with oxazolone. Each video sequence lasts for 30 minutes, with images captured at one-minute intervals, resulting in a total of 31 acquisitions per video.

The primary goal of this challenge is to classify the provided video-patches into two distinct categories:

  1. Video-patches where cells suddenly change their direction of movement (class 1): These videos contain cells that demonstrate sudden changes in their migratory paths.
  2. Video-patches without sudden changes in cell direction (class 0): These videos either show cells moving in a linear manner, remain stationary, or contain video with only the background and no visible cells.

The dataset comprises a total of 300 2D video-patches extracted from 48 different videos, representing both classes (n=180 class 0 and n=120 class 1). Each video-patch is a 2D projection along the z-axis of a 3D video sequence, carefully adjusted to a common contrast range to enhance the visibility of the biological processes. Additionally, all videos have been preprocessed to ensure a uniform pixel size of 0.8 µm. Video-patches are saved as RGB .avi files.

The dataset consists of 300 pairs of video-patches and their corresponding labels, divided as follows:

  • Training set: 210 video-patches (70%)
  • Phase 1 test set: 30 video-patches (10%)
  • Phase 2 test set: 60 video-patches (20%)

Each subset includes video patches extracted from different and independent IVM videos.

Evaluation

The evaluation metrics for the challenge are designed to comprehensively assess the models' performance in classifying video-patches. The metrics include:

  • Area Under the ROC Curve (AUC)
  • Sensitivity
  • Specificity
  • Balanced Accuracy

The final score will be calculated as:

score = 0.4*AUC + 0.2*(Precision+Recall+Balanced Accuracy)

The evaluation code will be made public later.

 

Rules of Participation

  • The data used to train algorithms may be restricted to the data provided by the challenge.
  • Participants must not manually annotate the test dataset to train a supervised model for phase 1 or 2 submissions.
  • All results will be made publicly available.
  • During the submission phase, participants will be asked to upload their model predictions (in terms of probabilities) and an abstract describing the methodology used (in Phase 2).
  • There is no monetary prize for the winners of the challenge.
  • Both AI-based and non-AI-based methods are allowed.

 

We will collaborate with participants to create a comprehensive journal article summarizing the key results and analyses from this challenge. Participants who submit valuable work are welcome to contribute to the publication, with up to three authors from each team being acknowledged.

In order for us to include you in our paper:

  • Please submit a detailed description of your solution with your final test phase submission.
  • You are welcome to submit additional paragraphs and figures about your submission via email (see the Contact info on the Organizers page).

Besides, we encourage all participants to independently submit their results without imposing any publication embargo.

 

👥 Organizers

  • Diego Ulisse Pizzagalli - Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
  • Rolf Krause - Euler Institute, Università della Svizzera Italiana, Lugano, Switzerland
  • Santiago Fernandez Gonzalez - Institute for research in biomedicine, Bellinzona, Switzerland
  • Raffaella Fiamma Cabini - Euler Institute, Università della Svizzera Italiana, Lugano, Switzerland
  • Elisa Palladino - Institute for research in biomedicine, Bellinzona, Switzerland
  • Enrico Moscatello - Euler Institute, Università della Svizzera Italiana, Lugano, Switzerland

 

For further details please contact This email address is being protected from spambots. You need JavaScript enabled to view it.

Artificial intelligence applied to intravital video microscopy, 4th edition
13 - 15 November 2024

This workshop will cover theoretical and practical aspects regarding the application of A.I. -based methods for the analysis of intravital imaging data.
We will focus on the migration and interaction of immune cells observed in vivo, explaining how to get accurate tracking analysis, or how to extract insights from videos without using cell tracking.
Moreover, we will discuss the importance of Open Source and Open Data resources.
The topics and tools presented in this workshop can be applied also for other imaging modalities and cell types but a basic knowledge in microscopy is recommended.

How: Online via Google meet

When: November 13th – 15th
9:00 - 17:00 Switzerland time zone

Registration: up to November 2nd 2024 23:59 CET
Cost: 150 CHF (approx. 150 EURO).
You will receive a confirmation and details for the payment via email by registering at this form

18 places available, served on a first come first served basis.

Contact: For questions do not hesitate to contact us at This email address is being protected from spambots. You need JavaScript enabled to view it. with the subject of the email ai-ivm2024

Organizers:
Prof. Santiago Fernandez Gonzalez
Prof. Rolf Krause
Dr. Diego Ulisse Pizzagalli

Temtative Program

DAY 1: November 13th. Introduction, intravital imaging and Open Data

Learning objectives. Understanding the applications and advantages of intravital microscopy / the importance of Open Data research / Practice with immunemap platform and other tools

09:00 - 10:00 Introduction
10:00 - 11:15 Principles of fluorescence and intravital microscopy
11:15 - 11:30 Coffee break
11:30 - 12:30 Studying the immune system in vivo, surgical models and applications
12:30 - 14:00 Lunch Break
14:00 - 16:00 Open Data research, FAIR principles and Immunemap

DAY 2: November 14th: Analysis with tracking. 

Learning objectives. Understanding what can be extracted from IVM data using the classical image analysis pipeline (tracking and track measures), challenges and new perspectives.

09:00 - 10:00 Cell motility and cell-to-cell interaction metrics.
10:30 - 10:45 Coffee break
10:45 - 12:30 Practical session 2: Exercises to quantify motility
12:30 - 14:00 Lunch Break
14:00 - 15:00 Tracking with FIJI/Trackmate
15:00 - 17:00 Image processing and supervised machine learning techniques to facilitate cell detection and tracking

DAY 3: November 15th: Analysis without tracking.

Learning objectives. Understanding how image processing and computer vision techniques can be applied to analyze IVM data without necessarily using of cell tracking

09:00 - 10:15 Recent trends in computer vision methods - discussion
10:15 - 10:30 Coffee break
10:30 - 12:00 Apoptosis detection via machine learning
12:00 - 13:00 Lunch Break
13:00 - 14:00 Unsupervised learning to identify motility patterns
14:00 - 16:00 Practical session 3: Analyzing cell migration without tracking
16:10 - 17:00 Conclusion

 

 

 

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API Documentation

These are the main APIs to interface with immunemap. Base URL is https://api.immunemap.org/

  • GET​/acquisition​/{id}
    function to get an Acquisition by Acquisition ID
  • GET​/acquisition​/video​/{video}
    function to get an Acquisition by video ID
  • GET​/video​/{video}
    function to get a video by Video ID
  • GET​/video​/acquisition​/{acquisition}
    function to get a video by Acquisition ID
  • GET​/video​/{video}​/tracks
    function to get a video tracks by Video ID
  • GET​/video​/​{video}/preview
    function to get the video preview file

 More details below.

Acquisition API Documentation

GET /acquisition/{id}

This endpoint allows you to retrieve information about a specific Acquisition entity by its unique identifier.

Resource URL

https://api.immunemap.org/acquisition/10

 

Parameters

  • {id} (required, integer) - The unique identifier of the Acquisition entity to retrieve. The {id} must be a positive integer.

Response

  • HTTP Status Code: 200 OK
  • Content Type: application/json

Example Response:

json

{

"id":10

"experimental_group":8

"name":"10 hours post vaccination"

"sequence":1

"area":"Lymph node"

"magnification":25

"notes":"intravital imaging using two-photon microscopy, of NK cells (green) and macrophages (red) in the lymph node, into a Ncr1-GFP animal, after UV-PR8 virus injection (white). "cell_stainings":

"video":17

"video_details":

                  "DB_id":17

                  "id":"37AXXPYHHN80XBCD4D57ENTKFA"

                  "uid":"37AXXPYHHN80XBCD4D57ENTKFA"

                  "owner":"This email address is being protected from spambots. You need JavaScript enabled to view it."

                  "author":"This email address is being protected from spambots. You need JavaScript enabled to view it."

                  "location":"\/srv\/immunemap\/backend\/public\/uploads\/c5637a29-40ed-4d88-89d5-405c5b63a474.data"

                  "size":

                                   "width":555

                                   "height":555

                                   "slices":16

                                   "frames":30

                                   "spacing":[0.8,0.8,3]

                                   "fps":0.01702620332692

                                   "number_of_channels":4

                                   "channel_configuration":

                                   "deleted":false

                  "created":

                                   "date":"2022-03-10 14:38:37.000000","timezone_type":3,"timezone":"UTC"

                  "recorded":

                  "date":"2014-09-30 16:56:42.000000","timezone_type":3,"timezone":"UTC"

                  "notes":

                  "time_steps":

                  "annotations":[]

                  "uploaded_from":"10.25.11.22"

                  "uploaded_on":{"date":"2022-03-10 14:38:37.000000","timezone_type":3,"timezone":"UTC"}

                  "size":854447056,

                  "name":"15-27-16.ims"

                  "upload_status":4

"tags":

                  {"value":"collagen"}

                  {"value":"follicular-dendritic-cells"}

                  {"value":"influenza"}

                  {"value":"influenza-a"}

                  {"value":"macrophages"}

                  {"value":"natural-killer-cells"}

                  {"value":"vaccination"}]

"links":

"mouseId":"0"

"official_mouse_name":

"gender":"male"

 

}

 

Authorization

This endpoint requires the user to have the VIEW permission on the specified Acquisition entity. Users without this permission will receive a 403 Forbidden response.

Request Example

You can make a GET request to this endpoint to retrieve information about a specific Acquisition entity. Replace {id} with the actual identifier of the Acquisition you want to retrieve.

http

GET /acquisition/10

 

 

 

 

Error Responses

  • HTTP Status Code: 404 Not Found
    If the specified Acquisition entity with the given ID does not exist, the API will return a 404 Not Found
  • HTTP Status Code: 403 Forbidden
    If the user does not have the VIEW permission on the specified Acquisition entity, the API will return a 403 Forbidden

 

 

Acquisition by Video ID API Documentation

GET /acquisition/video/{videoId}

This endpoint allows you to retrieve Acquisitions associated with a specific Video by its unique identifier.

Resource URL

https://api.immunemap.org/acquisition/video/17

Parameters

  • {videoId} (required, integer) - The unique identifier of the Video entity to retrieve associated Acquisitions. The {videoId} must be a positive integer.

Response

  • HTTP Status Code: 200 OK
  • Content Type: application/json

Example Response:

json

{

"id":10

"experimental_group":8

"name":"10 hours post vaccination"

"sequence":1

"area":"Lymph node"

"magnification":25

"notes":"intravital imaging using two-photon microscopy, of NK cells (green) and macrophages (red) in the lymph node, into a Ncr1-GFP animal, after UV-PR8 virus injection (white). "cell_stainings":

"video":17

"video_details":

                  "DB_id":17

                  "id":"37AXXPYHHN80XBCD4D57ENTKFA"

                  "uid":"37AXXPYHHN80XBCD4D57ENTKFA"

                  "owner":"This email address is being protected from spambots. You need JavaScript enabled to view it."

                  "author":"This email address is being protected from spambots. You need JavaScript enabled to view it."

                  "location":"\/srv\/immunemap\/backend\/public\/uploads\/c5637a29-40ed-4d88-89d5-405c5b63a474.data"

                  "size":

                                   "width":555

                                   "height":555

                                   "slices":16

                                   "frames":30

                                   "spacing":[0.8,0.8,3]

                                   "fps":0.01702620332692

                                   "number_of_channels":4

                                   "channel_configuration":

                                   "deleted":false

                  "created":

                                   "date":"2022-03-10 14:38:37.000000","timezone_type":3,"timezone":"UTC"

                  "recorded":

                  "date":"2014-09-30 16:56:42.000000","timezone_type":3,"timezone":"UTC"

                  "notes":

                  "time_steps":

                  "annotations":[]

                  "uploaded_from":"10.25.11.22"

                  "uploaded_on":{"date":"2022-03-10 14:38:37.000000","timezone_type":3,"timezone":"UTC"}

                  "size":854447056,

                  "name":"15-27-16.ims"

                  "upload_status":4

"tags":

                  {"value":"collagen"}

                  {"value":"follicular-dendritic-cells"}

                  {"value":"influenza"}

                  {"value":"influenza-a"}

                  {"value":"macrophages"}

                  {"value":"natural-killer-cells"}

                  {"value":"vaccination"}]

"links":

"mouseId":"0"

"official_mouse_name":

"gender":"male"

 

}

 

Authorization

This endpoint requires the user to have the VIEW permission on the specified Video entity. Users without this permission will receive a 403 Forbidden response.

Request Example

You can make a GET request to this endpoint to retrieve Acquisitions associated with a specific Video. Replace {videoId} with the actual identifier of the Video you want to retrieve acquisitions for.

http

GET /acquisition/video/57

 

 

Error Responses

  • HTTP Status Code: 404 Not Found
    If the specified Video entity with the given ID does not exist, the API will return a 404 Not Found
  • HTTP Status Code: 403 Forbidden
    If the user does not have the VIEW permission on the specified Video entity, the API will return a 403 Forbidden

 

 

Video by Video ID API Documentation

GET /video/{videoId}

This endpoint allows you to retrieve information about a specific Video entity by its unique identifier.

Resource URL

bash

https://api.immunemap.org/video/17

 

Parameters

  • {videoId} (required, integer) - The unique identifier of the Video entity to retrieve. The {videoId} must be a positive integer.

Response

  • HTTP Status Code: 200 OK
  • Content Type: application/json

Example Response:

json

{

"DB_id":17

"id":"37AXXPYHHN80XBCD4D57ENTKFA"

                  "uid":"37AXXPYHHN80XBCD4D57ENTKFA"

                  "owner":"This email address is being protected from spambots. You need JavaScript enabled to view it."

                  "author":"This email address is being protected from spambots. You need JavaScript enabled to view it.

"location":"\/srv\/immunemap\/backend\/public\/uploads\/c5637a29-40ed-4d88-89d5-405c5b63a474.data"

"video_details":

                  "size":

                                   "width":555

                                   "height":555

                                   "slices":16

                                   "frames":30

                                   "spacing":[0.8,0.8,3]

                                   "fps":0.01702620332692

                                   "number_of_channels":4

                                   "channel_configuration":

                                   "deleted":false

                  "created":

                                   "date":"2022-03-10 14:38:37.000000","timezone_type":3,"timezone":"UTC"

                  "recorded":

                  "date":"2014-09-30 16:56:42.000000","timezone_type":3,"timezone":"UTC"

                  "notes":

                  "time_steps":

                  "annotations":[]

                  "uploaded_from":"10.25.11.22"

                  "uploaded_on":{"date":"2022-03-10 14:38:37.000000","timezone_type":3,"timezone":"UTC"}

                  "size":854447056,

                  "name":"15-27-16.ims"

                  "upload_status":4

 

}

Authorization

This endpoint requires the user to have the VIEW permission on the specified Video entity. Users without this permission will receive a 403 Forbidden response.

Request Example

You can make a GET request to this endpoint to retrieve information about a specific Video entity. Replace {videoId} with the actual identifier of the Video you want to retrieve.

http

GET /video/17

 

Error Responses

  • HTTP Status Code: 404 Not Found
    If the specified Video entity with the given ID does not exist, the API will return a 404 Not Found
  • HTTP Status Code: 403 Forbidden
    If the user does not have the VIEW permission on the specified Video entity, the API will return a 403 Forbidden

 

 

 

Video by Acquisition ID API Documentation

GET video/acquisition/{acquisitionId}

This endpoint allows you to retrieve the Video associated with a specific Acquisition entity by its unique identifier.

Resource URL

https://api.immunemap.org/video/acquisition/10

Parameters

  • {acquisitionId} (required, integer) - The unique identifier of the Acquisition entity for which you want to retrieve the associated Video. The {acquisitionId} must be a positive integer.

Response

  • HTTP Status Code: 200 OK
  • Content Type: application/json

Example Response:

json

{

"DB_id":17

"id":"37AXXPYHHN80XBCD4D57ENTKFA"

                  "uid":"37AXXPYHHN80XBCD4D57ENTKFA"

                  "owner":"This email address is being protected from spambots. You need JavaScript enabled to view it."

                  "author":"This email address is being protected from spambots. You need JavaScript enabled to view it.

"location":"\/srv\/immunemap\/backend\/public\/uploads\/c5637a29-40ed-4d88-89d5-405c5b63a474.data"

"video_details":

                  "size":

                                   "width":555

                                   "height":555

                                   "slices":16

                                   "frames":30

                                   "spacing":[0.8,0.8,3]

                                   "fps":0.01702620332692

                                   "number_of_channels":4

                                   "channel_configuration":

                                   "deleted":false

                  "created":

                                   "date":"2022-03-10 14:38:37.000000","timezone_type":3,"timezone":"UTC"

                  "recorded":

                  "date":"2014-09-30 16:56:42.000000","timezone_type":3,"timezone":"UTC"

                  "notes":

                  "time_steps":

                  "annotations":[]

                  "uploaded_from":"10.25.11.22"

                  "uploaded_on":{"date":"2022-03-10 14:38:37.000000","timezone_type":3,"timezone":"UTC"}

                  "size":854447056,

                  "name":"15-27-16.ims"

                  "upload_status":4

 

}

 

Authorization

This endpoint requires the user to have the VIEW permission on the associated Video entity. Users without this permission will receive a 403 Forbidden response.

Request Example

You can make a GET request to this endpoint to retrieve the Video associated with a specific Acquisition entity. Replace {acquisitionId} with the actual identifier of the Acquisition entity for which you want to retrieve the associated Video.

http

GET video/acquisition/10

 

Error Responses

  • HTTP Status Code: 404 Not Found
    If the specified Acquisition entity with the given ID does not exist or does not have an associated Video, the API will return a 404 Not Found
  • HTTP Status Code: 403 Forbidden
    If the user does not have the VIEW permission on the associated Video entity, the API will return a 403 Forbidden

 

 

Video Tracks by Video ID API Documentation

GET /video/{videoId}/tracks

This endpoint allows you to retrieve the tracks associated with a specific Video entity by its unique identifier.

Resource URL

https://api.immunemap.org/video/17/tracks

Parameters

  • {videoId} (required, integer) - The unique identifier of the Video entity for which you want to retrieve the associated tracks. The {videoId} must be a positive integer.

Response

  • HTTP Status Code: 200 OK
  • Content Type: application/json

Example Response:

json

{

"id":44639

"label":"15-27-16_1ime0000_ct1.csv_0"

"color":"#FFFF00"

"author":6

"video":17

"date":{"date":"2022-06-29 00:00:00.000000","timezone_type":3,"timezone":"UTC"}

"points":[[0,6.5,459.5,1],[1,3.25,463.25,1],[2,4.25,467.75,1],[3,3.25,478.5,1],[4,3,479.25,1]]

"cellTypeObject":null

"cellTypeName":"NK cells"

 

}

Authorization

This endpoint requires the user to have the VIEW permission on the specified Video entity. Users without this permission will receive a 403 Forbidden response.

 

Request Example

You can make a GET request to this endpoint to retrieve the tracks associated with a specific Video entity. Replace {videoId} with the actual identifier of the Video for which you want to retrieve tracks.

http

GET /video/17/tracks

Error Responses

  • HTTP Status Code: 404 Not Found
    If the specified Video entity with the given ID does not exist, or it does not have associated tracks, the API will return a 404 Not Found
  • HTTP Status Code: 403 Forbidden
    If the user does not have the VIEW permission on the specified Video entity, the API will return a 403 Forbidden

 

 

 

Video Preview File API Documentation

GET /video/{videoId}/preview

This endpoint allows you to retrieve the preview file of a specific Video entity by its unique identifier.

Resource URL

https://api.immunemap.org/video/17/preview

Parameters

  • {videoId} (required, integer) - The unique identifier of the Video entity for which you want to retrieve the preview file. The {videoId} must be a positive integer.

Response

  • HTTP Status Code: 200 OK
  • Content Type: video/mp4 (MPEG-4 video file)

Authorization

This endpoint requires the user to have the VIEW permission on the specified Video entity. Users without this permission will receive a 403 Forbidden response.

Request Example

You can make a GET request to this endpoint to retrieve the preview file of a specific Video entity. Replace {videoId} with the actual identifier of the Video for which you want to retrieve the preview file. You can also include the forceCreate query parameter if needed.

http

GET /video/17/preview

 

 

Response

If the request is successful, you will visualize a video player with the preview.

Error Responses

  • HTTP Status Code: 404 Not Found
    If the specified Video entity with the given ID does not exist, the API will return a 404 Not Found
  • HTTP Status Code: 403 Forbidden
    If the user does not have the VIEW permission on the specified Video entity, the API will return a 403 Forbidden
  • HTTP Status Code: 500 Internal Server Error
    If an error occurs during the retrieval or creation of the preview file, the API will return a 500 Internal Server Error

 

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