ScanGrow Manuscript files

Datasets relative to the manuscript describing the ScanGrow [Proof of Concept] application: ----------------------------------------------------------------------------- Worth RM and Espina L (2022) ScanGrow: Deep Learning-Based Live Tracking of Bacterial Growth in Broth. Front. Microbiol. 13:900596. doi: 10.3389/fmicb.2022.900596 ----------------------------------------------------------------------------- The contents of the three compressed folders are described below. 1. TRAINING_MODEL.ZIP Collection of images and spreadsheets that was used in the training of the image classification model that ScanGrow [PoC] uses by default. This training dataset should be subjected to the pre-processing workflow provided with ScanGrow to obtain the grouped images to be fed to the model training utility. 2. TEST_MODEL.ZIP Collection of images and spreadsheets comprising the Test dataset used in the evaluation of the image classification model. This includes: - New scans and spreadsheets (represented in Figure 3 as gray triangles). - Evaluation.csv: combined results of the output files from command "Test Model" when run with: * Dataset Test: these scans and spreadsheets (not used for training), * Dataset Training: the dataset used for training the model, or * Dataset Validation: the Training dataset after having flipped horizontally and offsetting the images and adjusted the spectrophotometric values according to the newly inverted well positions. 3. SAMPLE_RUN.ZIP Data from a sample run used to test ScanGrow on a microplate containing different concentrations of several antibiotics. This includes: - Scans used to in the "Sample run" with added antibiotics in the bacterial cultures. - Sample_run_raw.csv: Data exported from the Table view after the run. - Sample_run_processed.csv: Data from the Sample_run_raw.csv file after the introduction of metadata (eg. contents of each well) and calculation of the AUC (area under the curve). - Sample_run_json.json: JSON file showing the results of this run. It can be loaded into a ScanGrow session by clicking on "Show Graphs" -> "Open". - ImageMask.csv: alternative ImageMask to substitute the original one in "C:\Program Files\Riverwell Consultancy Services Ltd\Scan Grow\Configuration". In this alternative ImageMask file, well C11 was modified to overcome an artefact in the scan.