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| # Larvae Counter User Guide | |
| Welcome! This is a web-app that is equipped with a variety of tools to automate the counting | |
| of mosquito larvae and pupae (although mostly pupae at this stage) from images. Currently, this | |
| larvae counting tool has three automatic pupae counting tools based on "old-school" computer | |
| vision techniques. However, a deep-learning method based off of the `YoloV8` architecture | |
| is currently in development. Hypothetically, this deep learning method should be much less | |
| susceptible to noise and allow the simultaneous counting of larvae and pupae, and maybe even | |
| other stages of the mosquito life cycle. See below for a quick getting started guide. | |
| ## Workflow | |
| Below is the general workflow used to count mosquito larvae present in an image. | |
| ### Step 1: Upload an Image | |
| The first step is to upload an image containing pupae to be counted. This is done by either | |
| clicking on or dragging an image file to the camera icon on the page. If this app is being | |
| used on a smartphone an image can also be taken directly from the smartphone's camera by | |
| tapping on the camera icon. After uploading an image, you can begin tunning parameters. | |
| ### Step 2: Parameter Tuning | |
| The next step is select your counting method and begin tuning the counting parameters. The | |
| counting method can be selected in the drop-down list below the image upload box. The | |
| `Gradient CC w/ filter` is recommended as the default counting algorithm. The parameters | |
| for the selected counting method can be found in the box below the counting method drop-down | |
| list. | |
| It is recommend to click the `count` button with the default parameters to get a general | |
| idea of how the parameters need to be changed in order to get better results. After changing | |
| the parameters, click the `count` button again to re-run the selected algorithm with a new | |
| set of parameters. | |
| In general, parameters should be tuned from top down - meaning that the first parameter from the | |
| top should be tuned to get satisfactory results, then the second parameter, and so on. The | |
| images provided in the `Visualization` section of the results box (below the parameters box) | |
| should be used to tune the parameters. More details will be given on each counting method and | |
| its parameters below. | |
| ### Step 3: Check Results | |
| After the parameters have been tuned, the final results are available in the results box - which | |
| is situated just below the counting parameters box. | |
| ## Counting Algorithms | |
| The larvae-count tool currently has three counting algorithms available, `Gradient CC w/ Filter`, | |
| `Gradient CC`, and `Countour`. | |
| ### Gradient CC w/ filter | |
| `Gradient CC w/ Filter` (short for Gradient Connected Components with Elliptical Filter) counts | |
| the pupae present in an image utilizing clusters. The algorithm first creates a gray scale image | |
| from the provided image and applies a simple threshold in order to find pixels that are in a region | |
| containing pupae. A filter is then applied to filter out any pixels flagged as pupae that aren't part | |
| of a roughly elliptical pixel region. The algorithm than iterates over each overlapping cluster of | |
| pupae (hence the connected components) and calculated the number of pupae in each cluster by | |
| the area of the cluster in pixels. | |
| #### Parameters | |
| - `Color Threshold`: Cutoff below which a pixel in the gray-scale image will be considered to be | |
| in a region containing pupae. The allowed values range from (0-255). | |
| - `Average Area`: Average area (in pixels) of one pupae. | |
| - `Max Pupae Per Cluster (Optional)`: Maximum number of pupae per cluster, used to filter out any | |
| large dark blobs in the image. | |
| - `Filter Kernel Width (Pixels)`: Width (in pixels) of the elliptical filter. | |
| - `Filter Kernel Height (Pixels)`: Height (in pixels) of the elliptical filter. | |
| ### Gradient CC | |
| Same as `Gradient CC w/ Filter` but without the elliptical filter. | |
| #### Parameters | |
| - `Color Threshold`: Cutoff below which a pixel in the gray-scale image will be considered to be | |
| in a region containing pupae. The allowed values range from (0-255). | |
| - `Average Area`: Average area (in pixels) of one pupae. | |
| - `Max Pupae Per Cluster (Optional)`: Maximum number of pupae per cluster, used to filter out any | |
| large dark blobs in the image. | |
| ### Gradient Contour w/ Filter | |
| Similar to `Gradient CC w/ Filter`, but instead of iterating over every blob of "pupae pixels" | |
| it iterates over regions contained within (an) elliptical contour(s). | |
| #### Parameters | |
| - `Color Threshold`: Cutoff below which a pixel in the gray-scale image will be considered to be | |
| in a region containing pupae. The allowed values range from (0-255). | |
| - `Average Area`: Average area (in pixels) of one pupae. | |
| - `Max Pupae Per Cluster (Optional)`: Maximum number of pupae per cluster, used to filter out any | |
| large dark blobs in the image. | |
| - `Filter Kernel Width (Pixels)`: Width (in pixels) of the elliptical filter. | |
| - `Filter Kernel Height (Pixels)`: Height (in pixels) of the elliptical filter. |