egrace479 hlapp commited on
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Improves and completes the BibTeX record (#3)

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- Improves and completes the BibTeX record (145093363694284b89ead84f6fe3e3671cdb095b)
- Put BibTex in code block and fixed latex renders. (cb11a0061e768083a91ced933bb9703cb6bc3c7d)
- Fixed latex renders. (8b98cf2af795ec1357c58febd3de7bd29a7165ce)


Co-authored-by: Hilmar <hlapp@users.noreply.huggingface.co>

Files changed (1) hide show
  1. README.md +14 -15
README.md CHANGED
@@ -167,7 +167,7 @@ These arguments are meant to simplify adding `gen_metadata.py` to a workflow tha
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  ### Running with Singularity
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- A Docker container is automatically built for each **drexel_metadata** release. This container has the requirements installed and includes the model file.
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  To run the singularity container for a specific version follow this pattern:
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  ```
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  singularity run docker://ghcr.io/hdr-bgnn/drexel_metadata:<release> gen_metadata.py ...
@@ -291,18 +291,17 @@ J. Pepper, J. Greenberg, Y. Bakiş, X. Wang, H. Bart and D. Breen, "Automatic Me
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  **BibTeX:**
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-
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  @article{KPB2022,
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-
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- title = "Computational metadata generation methods for biological specimen image collections",
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-
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- author = "Karnani, K. and Pepper, J. and Bakiş, Y. and et al.",
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-
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- journal = "Int J Digit Libr",
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-
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- year = "2022"
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-
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  }
 
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  <!--
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  **APA:**
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@@ -319,7 +318,7 @@ J. Pepper, J. Greenberg, Y. Bakiş, X. Wang, H. Bart and D. Breen, "Automatic Me
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  | fish\_count | Overall Image | Integer | The quantity of fish present. |
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  | has\_ruler | Overall Image | Boolean | Whether a ruler was found in the image. |
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  | ruler\_bbox | Overall Image | 4 Tuple | The bounding box of the ruler (if found). |
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- | scale* | Overall Image | Float | The scale of the image in $\frac{\mathrm{pixels}}{\mathrm{cm}}$. |
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  | bbox | Per Fish | 4 Tuple | The top left and bottom right coordinates of the bounding box for a fish. |
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  | background.mean | Per Fish | Float | The mean intensity of the background within a given fish's bounding box. |
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  | background.std | Per Fish | Float | The standard deviation of the background within a given fish's bounding box. |
@@ -336,12 +335,12 @@ J. Pepper, J. Greenberg, Y. Bakiş, X. Wang, H. Bart and D. Breen, "Automatic Me
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  | has\_eye | Per Fish | Boolean | Whether an eye was found for a given fish. |
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  | eye\_center | Per Fish | 2 Tuple | The centroid of a fish's eye. |
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  | side* | Per Fish | String | The side (i.e. 'left' or 'right') of the fish that is facing the camera (dependent on finding its eye). |
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- | area | Per Fish | Float | Area of fish in $\mathrm{cm^2}$. |
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  | cont\_length | Per Fish | Float | The longest contiguous length of the fish in centimeters. |
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  | cont\_width | Per Fish | Float | The longest contiguous width of the fish in centimeters. |
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- | convex\_area | Per Fish | Float | Area of convex hull image (smallest convex polygon that encloses the fish) in $\mathrm{cm^2}$. |
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  | eccentricity | Per Fish | Float | Ratio of the focal distance over the major axis length of the ellipse that has the same second-moments as the fish. |
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- | extent | Per Fish | Float | Ratio of pixels of fish to pixels in the total bounding box. Computed as $\frac{\mathrm{area}}{\mathrm{rows} * \mathrm{cols}}$ |
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  | feret\_diameter\_max | Per Fish | Float | The longest distance between points around the fish’s convex hull contour. |
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  | kurtosis | Per Fish | 2D Vector | The sharpness of the peaks of the frequency-distribution curve of mask pixel coordinates. |
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  | major\_axis\_length | Per Fish | Float | The length of the major axis of the ellipse that has the same normalized second central moments as the fish. |
 
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  ### Running with Singularity
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+ A Docker container is automatically built for each **drexel\_metadata** release. This container has the requirements installed and includes the model file.
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  To run the singularity container for a specific version follow this pattern:
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  ```
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  singularity run docker://ghcr.io/hdr-bgnn/drexel_metadata:<release> gen_metadata.py ...
 
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  **BibTeX:**
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+ ```
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  @article{KPB2022,
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+ title = "Computational metadata generation methods for biological specimen image collections",
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+ author = "Karnani, Kevin and Pepper, Joel and Bak{\i}{\c s}, Yasin and Wang, Xiaojun and Bart, Jr, Henry and
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+ Breen, David E and Greenberg, Jane",
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+ journal = "International Journal on Digital Libraries",
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+ year = 2022,
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+ url = "https://doi.org/10.1007/s00799-022-00342-1",
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+ doi = "10.1007/s00799-022-00342-1"
 
 
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  }
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+ ```
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  <!--
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  **APA:**
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  | fish\_count | Overall Image | Integer | The quantity of fish present. |
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  | has\_ruler | Overall Image | Boolean | Whether a ruler was found in the image. |
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  | ruler\_bbox | Overall Image | 4 Tuple | The bounding box of the ruler (if found). |
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+ | scale* | Overall Image | Float | The scale of the image in \\(\frac{\mathrm{pixels}}{\mathrm{cm}}\\). |
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  | bbox | Per Fish | 4 Tuple | The top left and bottom right coordinates of the bounding box for a fish. |
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  | background.mean | Per Fish | Float | The mean intensity of the background within a given fish's bounding box. |
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  | background.std | Per Fish | Float | The standard deviation of the background within a given fish's bounding box. |
 
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  | has\_eye | Per Fish | Boolean | Whether an eye was found for a given fish. |
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  | eye\_center | Per Fish | 2 Tuple | The centroid of a fish's eye. |
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  | side* | Per Fish | String | The side (i.e. 'left' or 'right') of the fish that is facing the camera (dependent on finding its eye). |
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+ | area | Per Fish | Float | Area of fish in \\(\mathrm{cm^2}\\). |
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  | cont\_length | Per Fish | Float | The longest contiguous length of the fish in centimeters. |
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  | cont\_width | Per Fish | Float | The longest contiguous width of the fish in centimeters. |
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+ | convex\_area | Per Fish | Float | Area of convex hull image (smallest convex polygon that encloses the fish) in \\(\mathrm{cm^2}\\). |
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  | eccentricity | Per Fish | Float | Ratio of the focal distance over the major axis length of the ellipse that has the same second-moments as the fish. |
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+ | extent | Per Fish | Float | Ratio of pixels of fish to pixels in the total bounding box. Computed as \\(\frac{\mathrm{area}}{\mathrm{rows} * \mathrm{cols}}\\) |
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  | feret\_diameter\_max | Per Fish | Float | The longest distance between points around the fish’s convex hull contour. |
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  | kurtosis | Per Fish | 2D Vector | The sharpness of the peaks of the frequency-distribution curve of mask pixel coordinates. |
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  | major\_axis\_length | Per Fish | Float | The length of the major axis of the ellipse that has the same normalized second central moments as the fish. |