The IPP is a Web portal for biologists to interact with High Performance Compute (HPC) systems. Designed and funded by the IMB Microscopy Facility & the Research Computing Centre (RCC)
Create a GUI interface for stitching groups of images into one large image using Terastitcher or similar.
Spatial Transcriptomics pipeline
Select the files to process
Copy and/or Move and rename files to required location for deconvolution (optional)
Deconvolve the images using the parameters read by the metadata scraper (optional)
Save images in required format and file naming/folder structure for Stitching
Stitch the Images using metadata obtained from the scraper and user input using CPU or GPU on 1 or more nodes
Save the images to a QuPath readable format and file naming/folder structure
Analyse the images using QuPath scripts
Save the output
Interactive filebrowser (may require the ability for the user to specify the dimension naming format of the files) to select single or multiple files (may be in a complex folder structure or a single folder) and move them into the file/folder structure required for deconvolution. May need to additionally rename the moved files so Batch Deconvolution can process them. Standard instrument output files could be automatically detected using the metadata scraper, or from a dropdown list the user navigates to determine the naming convention and file/folder structure of the input files. Process the input files using the metadata scraper read required parameters and any other parameters entered by the user
Create a GUI interface for stitching groups of images into one large image using Terastitcher or similar.
Spatial Transcriptomics pipeline
Select the files to process Copy and/or Move and rename files to required location for deconvolution (optional) Deconvolve the images using the parameters read by the metadata scraper (optional) Save images in required format and file naming/folder structure for Stitching Stitch the Images using metadata obtained from the scraper and user input using CPU or GPU on 1 or more nodes Save the images to a QuPath readable format and file naming/folder structure Analyse the images using QuPath scripts Save the output Interactive filebrowser (may require the ability for the user to specify the dimension naming format of the files) to select single or multiple files (may be in a complex folder structure or a single folder) and move them into the file/folder structure required for deconvolution. May need to additionally rename the moved files so Batch Deconvolution can process them. Standard instrument output files could be automatically detected using the metadata scraper, or from a dropdown list the user navigates to determine the naming convention and file/folder structure of the input files. Process the input files using the metadata scraper read required parameters and any other parameters entered by the user