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Video contest
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🔍 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:
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:
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:
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:
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:
Each subset includes video patches extracted from different and independent IVM videos.
The evaluation metrics for the challenge are designed to comprehensively assess the models' performance in classifying video-patches. The metrics include:
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
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:
Besides, we encourage all participants to independently submit their results without imposing any publication embargo.
👥 Organizers
For further details please contact This email address is being protected from spambots. You need JavaScript enabled to view it.
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
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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These are the main APIs to interface with immunemap. Base URL is https://api.immunemap.org/
More details below.
This endpoint allows you to retrieve information about a specific Acquisition entity by its unique identifier.
https://api.immunemap.org/acquisition/10
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"
}
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.
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
This endpoint allows you to retrieve Acquisitions associated with a specific Video by its unique identifier.
https://api.immunemap.org/acquisition/video/17
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"
}
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.
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
This endpoint allows you to retrieve information about a specific Video entity by its unique identifier.
bash
https://api.immunemap.org/video/17
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
}
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.
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
This endpoint allows you to retrieve the Video associated with a specific Acquisition entity by its unique identifier.
https://api.immunemap.org/video/acquisition/10
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
}
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.
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
This endpoint allows you to retrieve the tracks associated with a specific Video entity by its unique identifier.
https://api.immunemap.org/video/17/tracks
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"
}
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.
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
This endpoint allows you to retrieve the preview file of a specific Video entity by its unique identifier.
https://api.immunemap.org/video/17/preview
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.
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
If the request is successful, you will visualize a video player with the preview.
Error Responses