PaulRitsche · PaulRitsche · Nov 19, 2024 · Nov 2, 2024 · Nov 2, 2024
diff --git a/.gitignore b/.gitignore
@@ -205,4 +205,7 @@ $RECYCLE.BIN/
 webapp/.streamlit/
 
 # MongoDB
-access.txt
+access.txt
+
+# Benchmarks
+benchmarks/
diff --git a/webapp/database.py b/webapp/database.py
@@ -22,53 +22,69 @@
 # Example data
 dictionary = [
     {
-        "DATASET_NAME": "FALLMUD_2017",  # Name the dataset accordingly
+        "DATASET_NAME": "DeepMTJ_2021",  # Name the dataset accordingly
         "DOI": None,  # Provide a DOI
         "VERSION": 1.0,  # Version of the dataset
         "MUSCLE": [
-            "Gastrocnemius",
-            "Soleus",
+            "Gastrocnemius medialis",
+            "Gastrocnemius lateralis",
         ],  # What muscle is included in the dataset? If more than one, split the dataset into multiple parts
-        "MUSCLE_REGION": "middle",  # Which muscle regions are included in the dataset?
-        "DEVICE": "AlokaSSD-5000 PHD 7.5 MHz",  # What US device was used?
-        "PROBE": None,  # What probe was used?
+        "MUSCLE_REGION": "distal",  # Which muscle regions are included in the dataset?
+        "DEVICE": [
+            "Aixplorer V6, SuperSonic Imagine, Aix-en-Provence, France",
+            "MyLab 60, Esoate Biomedical, Genova, Italy",
+            "ArtUs EXT-1H, TELEMED, Milan, Italy ",
+        ],  # What US device was used?
+        "PROBE": [
+            "linear-array 90mm, LA923",
+            "linear-array 60mm, LV8-5N60-A2",
+            "linear-array 38-mm probe, Superline SL10-2",
+        ],  # What probe was used?
         "DATA_TYPE": "images",  # Does the dataset contain images, videos, or volumes?
-        "FILE_TYPE": "jpg",  # What is the file type of the data?
+        "FILE_TYPE": "jpeg",  # What is the file type of the data?
         "IMAGE_TYPE": "static",  # If images are included, are they static or panoramic?
-        "DATA_PLANE": "longitudinal",  # In what plane were the images/videos collected?
-        "PARTICIPANT_AGE": 30,  # Mean age of participants.
+        "DATA_PLANE": "Longitudinal",  # In what plane were the images/videos collected?
+        "PARTICIPANT_AGE": None,  # Mean age of participants.
         "PARTICIPANT_HEIGHT": None,  # Mean height of participants (in cm).
         "PARTICIPANT_WEIGHT": None,  # Mean weight of participants (in kg).
         "PARTICIPANT_SEX": "both",  # Included males, females, or both?
-        "SAMPLE_SIZE": 8,  # How many participants are included in the dataset?
+        "SAMPLE_SIZE": "161",  # How many participants are included in the dataset?
         "DATA_LABELS": True,  # Are labels provided for the data?
-        "DATA_LABELS_DESCRIPTION": "The labels are provided as binary masks.",  # If labels are provided, what is the format of the labels?
-        "SHORT_DESCRIPTION": "This dataset presents an investigation into the feasibility of using deep learning methods for developing abitrary full spatial resolution regression analysis of B-mode ultrasound images of human skeletal muscle. Dynamic ultrasound images sequences of the calf muscles were acquired (25 Hz) from 8 healthy volunteers (4 male, ages: 25–36, median 30). Here, the labels correspond to the extrapolated fascicles including curvature, not only visible fascicle fragments. ",  # Describe the data in 3-4 sentences.
-        "DATASET_YEAR": 2017,  # What year was the dataset created?
-        "PUBLICATION_LINK": "https://www.mdpi.com/2313-433X/4/2/29",  # Can you provide a link to the publication containing the data?
+        "DATA_LABELS_DESCRIPTION": "Manually set labels in the training dataset denote exact pixel positions of estimated MTJ positions in the image and images were labelled by a total of four raters. For our training, we used soft labeling, where we assigned probability values to each image pixel. We used probability maps at the same resolution as original images, where we modeled positions of the MTJ by a 2D normal distribution with a covariance of 100 pixels at positions of specialist labels.",  # If labels are provided, what is the format of the labels?
+        "SHORT_DESCRIPTION": "Data were collected at the University of Graz, the Graz University of Technology and the University of Queensland between 2014 and 2020 on 123 healthy and 38 impaired individuals inclduing children and adults. With 1590 recordings, the isometric maximum voluntary contractions (MVC) and passive torque movements (PT) on the medial gastrocnemius (MG) had the largest share in the dataset. A smaller amount of data was collected on the MG during running (48 recordings). The measurements on the lateral gastrocnemius (LG) consist of 109 recordings. The complete and fully anonymous dataset holds 1747 video recordings with a mean length of 19.84 seconds per video. Sequences were captured at frame-rates of 30 frames per second (fps) for studies with an Aixplorer V6 (SuperSonic Imagine, Aix-en-Provence, France) US system (Aixplorer), 25 fps for studies with the Esaote MyLab60 system (Esaote), and 30-80 fps for the Telemed ArtUs US (Telemed), respectively. The scanning frequency varied between 7 to 9 MHz.",  # Describe the data in 3-4 sentences.
+        "DATASET_YEAR": "2021",  # What year was the dataset created?
+        "PUBLICATION_LINK": "10.1109/TBME.2021.3130548",  # Can you provide a link to the publication containing the data?
         "AUTHORS": [
-            "Ryan Cunningham",
-            "Maria B. Sanchez",
-            "Gregory May",
-            "Ian Loram",
+            "Christoph Leitner",
+            "Robert Jarolim",
+            "Bernhard Englmair",
+            "Annika Kruse",
+            "Karen Andrea Lara Hernandez",
+            "Andreas Konrad",
+            "Eric Yung-Sheng Su",
+            "Jorg Schrottner",
+            "Luke A Kelly",
+            "Glen A Lichtwark",
+            "Markus Tilp",
+            "Christian Baumgartner",
         ],  # Who are the authors of the data?
         "CONTACT": [
-            "M.Sanchez.Puccini@mmu.ac.uk",
-            "g.may@mmu.ac.uk",
+            "christoph.leitner@tugraz.at",
         ],  # Provide contact details of the authors.
-        "DATASET_LINK": "https://kalisteo.cea.fr/index.php/fallmud/",  # Will be provided by us if not already existent.
-        "LICENSE": "Attribution-NonCommercial 4.0 International",  # What is the license of the data?
-        "SCANNING_FREQUENCY": "7.5Hz",  # What is the scanning frequency of the data?
-        "SAMPLING_RATE": 25,  # What is the sampling rate or fps of the data collection?
+        "DATASET_LINK": "https://osf.io/wgy4d/",  # Will be provided by us if not already existent.
+        "LICENSE": "CC-By Attribution 4.0 International",  # What is the license of the data?
+        "SCANNING_FREQUENCY": None,  # What is the scanning frequency of the data?
+        "SAMPLING_RATE": 80,  # What is the sampling rate or fps of the data collection?
     }
 ]
 
+
 # Insert data into the collection
 # Uncomment the next line to insert template data into database
 collection.insert_many(dictionary)
 
 # Retrieve and print data from the collection
-query = {"DATASET_NAME": "FALLMUD_2017"}
+query = {"DATASET_NAME": "DeepMTJ_2021"}
 results = collection.find(query)
 
 # Print the result, DATASET_LINK must be present

diff --git a/webapp/database_entries/_dictionary_DL_Track_US_2023.py b/webapp/database_entries/_dictionary_DL_Track_US_2023.py
@@ -4,19 +4,19 @@
         "DOI": "10.17605/OSF.IO/7MJSC",  # Provide a DOI
         "VERSION": 1.0,  # Version of the dataset
         "MUSCLE": [
-            "Medial Gastrocnemius",
+            "Gastrocnemius medialis",
             "Soleus",
-            "Vastus Laterlis",
-            "Tibialis Anterior",
+            "Vastus laterlis",
+            "Tibialis anterior",
         ],  # What muscle is included in the dataset? If more than one, split the dataset into multiple parts
         "MUSCLE_REGION": [
             "middle",
         ],  # Which muscle regions are included in the dataset?
         "DEVICE": [
-            "Aloka Alpha-10 Hitachi Healthcare",
-            "ArtUS EXT-1H TELEMED",
-            "HD11 Philips Electronics",
-            "Echo Blaster 128 TELEMED",
+            "Aloka Alpha-10, Hitachi Healthcare, Tokyo, Japan",
+            "ArtUS EXT-1H, TELEMED, Milan, Italy",
+            "HD11, Philips Electronics, Amsterdam, Netherlands",
+            "Echo Blaster 128, TELEMED, Milan, Italy",
         ],  # What US device was used?
         "PROBE": None,  # What probe was used?
         "DATA_TYPE": "images",  # Does the dataset contain images, videos, or volumes?

diff --git a/webapp/database_entries/_dictionary_DeepACSA_2022.py b/webapp/database_entries/_dictionary_DeepACSA_2022.py
@@ -4,8 +4,8 @@
         "DOI": "10.17605/OSF.IO/A3U4V",  # Provide a DOI
         "VERSION": 1.0,  # Version of the dataset
         "MUSCLE": [
-            "Rectus Femoris",
-            "Vastus Lateralis",
+            "Rectus femoris",
+            "Vastus lateralis",
             "Gastrocnemius medialis",
             "Gastrocnemius lateralis",
         ],  # What muscle is included in the dataset? If more than one, split the dataset into multiple parts
@@ -15,8 +15,8 @@
             "distal",
         ],  # Which muscle regions are included in the dataset?
         "DEVICE": [
-            "ACUSON Juniper, linear-array 54-mm probe, 12 L3 Acuson 12 L3, SIEMENS Healthineers Erlangen, Germany",
-            "Aixplorer Ultimate, linear-array 38-mm probe, Superline SL10-2 Super- Sonic Imagine, Aix-en-Provence France",
+            "ACUSON Juniper, SIEMENS Healthineers Erlangen, Germany",
+            "Aixplorer Ultimate, SuperSonic Imagine, Aix-en-Provence, France",
             "Mylab 70, linear-array 47-mm probe, Esaote Biomedica, Genova, Italy",
         ],  # What US device was used?
         "PROBE": [
@@ -33,7 +33,7 @@
         "PARTICIPANT_WEIGHT": None,  # Mean weight of participants (in kg).
         "PARTICIPANT_SEX": "both",  # Included males, females, or both?
         "SAMPLE_SIZE": 153,  # How many participants are included in the dataset?
-        "DATA_LABELS": None,  # Are labels provided for the data?
+        "DATA_LABELS": True,  # Are labels provided for the data?
         "DATA_LABELS_DESCRIPTION": "The labels are provided as binary masks of the whole muscle anatomical cross-sectional area.",  # If labels are provided, what is the format of the labels?
         "SHORT_DESCRIPTION": "The DeepACSA dataset contains panoramic ultrasound images of the human rectus femoris (RF), vastus lateralis (VL), gastrocnemius medialis (GM) and lateralis (GL) muscles. A total of 1772 (including image augmentation) ultrasound images from 153 participants (age = 38.2 yr, range = 13–78). The images were acquired with the participants in supine (VL and RF) and prone (GM and GL) positions at multiple regions.",  # Describe the data in 3-4 sentences.
         "DATASET_YEAR": 2022,  # What year was the dataset created?

diff --git a/webapp/database_entries/_dictionary_DeepMTJ_2021.py b/webapp/database_entries/_dictionary_DeepMTJ_2021.py
@@ -0,0 +1,57 @@
+template_data = template_data = [
+    {
+        "DATASET_NAME": "Deep_MTJ_2021",  # Name the dataset accordingly
+        "DOI": None,  # Provide a DOI
+        "VERSION": 1.0,  # Version of the dataset
+        "MUSCLE": [
+            "Gastrocnemius medialis",
+            "Gastrocnemius lateralis",
+        ],  # What muscle is included in the dataset? If more than one, split the dataset into multiple parts
+        "MUSCLE_REGION": "distal",  # Which muscle regions are included in the dataset?
+        "DEVICE": [
+            "Aixplorer V6, SuperSonic Imagine, Aix-en-Provence, France",
+            "MyLab 60, Esoate Biomedical, Genova, Italy",
+            "ArtUs EXT-1H, TELEMED, Milan, Italy ",
+        ],  # What US device was used?
+        "PROBE": [
+            "linear-array 90mm, LA923",
+            "linear-array 60mm, LV8-5N60-A2",
+            "linear-array 38-mm probe, Superline SL10-2",
+        ],  # What probe was used?
+        "DATA_TYPE": "images",  # Does the dataset contain images, videos, or volumes?
+        "FILE_TYPE": "jpeg",  # What is the file type of the data?
+        "IMAGE_TYPE": "static",  # If images are included, are they static or panoramic?
+        "DATA_PLANE": "Longitudinal",  # In what plane were the images/videos collected?
+        "PARTICIPANT_AGE": None,  # Mean age of participants.
+        "PARTICIPANT_HEIGHT": None,  # Mean height of participants (in cm).
+        "PARTICIPANT_WEIGHT": None,  # Mean weight of participants (in kg).
+        "PARTICIPANT_SEX": "both",  # Included males, females, or both?
+        "SAMPLE_SIZE": 161,  # How many participants are included in the dataset?
+        "DATA_LABELS": True,  # Are labels provided for the data?
+        "DATA_LABELS_DESCRIPTION": "Manually set labels in the training dataset denote exact pixel positions of estimated MTJ positions in the image and images were labelled by a total of four raters. For our training, we used soft labeling, where we assigned probability values to each image pixel. We used probability maps at the same resolution as original images, where we modeled positions of the MTJ by a 2D normal distribution with a covariance of 100 pixels at positions of specialist labels.",  # If labels are provided, what is the format of the labels?
+        "SHORT_DESCRIPTION": "Data were collected at the University of Graz, the Graz University of Technology and the University of Queensland between 2014 and 2020 on 123 healthy and 38 impaired individuals inclduing children and adults. With 1590 recordings, the isometric maximum voluntary contractions (MVC) and passive torque movements (PT) on the medial gastrocnemius (MG) had the largest share in the dataset. A smaller amount of data was collected on the MG during running (48 recordings). The measurements on the lateral gastrocnemius (LG) consist of 109 recordings. The complete and fully anonymous dataset holds 1747 video recordings with a mean length of 19.84 seconds per video. Sequences were captured at frame-rates of 30 frames per second (fps) for studies with an Aixplorer V6 (SuperSonic Imagine, Aix-en-Provence, France) US system (Aixplorer), 25 fps for studies with the Esaote MyLab60 system (Esaote), and 30-80 fps for the Telemed ArtUs US (Telemed), respectively. The scanning frequency varied between 7 to 9 MHz.",  # Describe the data in 3-4 sentences.
+        "DATASET_YEAR": 2021,  # What year was the dataset created?
+        "PUBLICATION_LINK": "10.1109/TBME.2021.3130548",  # Can you provide a link to the publication containing the data?
+        "AUTHORS": [
+            "Christoph Leitner",
+            "Robert Jarolim",
+            "Bernhard Englmair",
+            "Annika Kruse",
+            "Karen Andrea Lara Hernandez",
            "Andreas Konrad",
+            "Eric Yung-Sheng Su",
+            "Jorg Schrottner",
+            "Luke A Kelly",
+            "Glen A Lichtwark",
+            "Markus Tilp",
+            "Christian Baumgartner",
+        ],  # Who are the authors of the data?
+        "CONTACT": [
+            "christoph.leitner@tugraz.at",
+        ],  # Provide contact details of the authors.
+        "DATASET_LINK": "https://osf.io/wgy4d/",  # Will be provided by us if not already existent.
+        "LICENSE": "CC-By Attribution 4.0 International",  # What is the license of the data?
+        "SCANNING_FREQUENCY": None,  # What is the scanning frequency of the data?
+        "SAMPLING_RATE": 80,  # What is the sampling rate or fps of the data collection?
+    }
+]
diff --git a/webapp/database_entries/_dictionary_FALLMUD_2017.py b/webapp/database_entries/_dictionary_FALLMUD_2017.py
@@ -4,11 +4,11 @@
         "DOI": None,  # Provide a DOI
         "VERSION": 1.0,  # Version of the dataset
         "MUSCLE": [
-            "Gastrocnemius",
+            "Gastrocnemius medialis",
             "Soleus",
         ],  # What muscle is included in the dataset? If more than one, split the dataset into multiple parts
         "MUSCLE_REGION": "middle",  # Which muscle regions are included in the dataset?
-        "DEVICE": "AlokaSSD-5000 PHD 7.5 MHz",  # What US device was used?
+        "DEVICE": "Aloka SSD-5000 PHD, Hitachi Healthcare, Tokyo, Japan",  # What US device was used?
         "PROBE": None,  # What probe was used?
         "DATA_TYPE": "images",  # Does the dataset contain images, videos, or volumes?
         "FILE_TYPE": "jpg",  # What is the file type of the data?
@@ -36,7 +36,7 @@
         ],  # Provide contact details of the authors.
         "DATASET_LINK": "https://kalisteo.cea.fr/index.php/fallmud/",  # Will be provided by us if not already existent.
         "LICENSE": "Attribution-NonCommercial 4.0 International",  # What is the license of the data?
-        "SCANNING_FREQUENCY": "7.5Hz",  # What is the scanning frequency of the data?
+        "SCANNING_FREQUENCY": "7.5 MHz",  # What is the scanning frequency of the data?
         "SAMPLING_RATE": 25,  # What is the sampling rate or fps of the data collection?
     }
 ]