Test datasets for the TGlow pipeline

ABSTRACT: This dataset contains everything needed to test the TGlow high content imaging pipeline. It contains the configuration files and data needed to run the pipeline and is intended to test the pipeline instalation was successful. The images contain two fields and two wells (spread over two plates) of Jurkat cells imaged over two cycles. For more details on TGlow and the pipeline, and what the files represent we refer to our manuscript and github page respectively. Image description Raw images from Revity Opera Phenix converted to plate/row/col/field.ome.tiff. The two cycles are represented as seperate plates in the pipeline input. The manifest_registration controls which cycles get matched together. It contains two wells each with two fields containing Jurkat cells, imaged on an Opera Phenix Plus using 40x water objective, 16 z-planes at a resolution of 2160x2160 in x and y. The pixel sizes are 0.8x0.149x0.149um.  Inputs: manifests These control what goes into the pipeline and how it is excecuted, and what channels are used for which task. See the documentation for details Inputs: psfs The PSFs match the aquisition here and were generated by imaging beads using the same plates, coating and microscope settings. One note is the z-spacing is 100nm in the PSFs wheras it is 800nm in the raw images. Make sure to set the pipelines psf_subsample_z to 8 to sample every 8 planes from the middle so the z-spacing matches.

ORGANISM(S): Homo sapiens (human)

SUBMITTER: Olivier B. Bakker 

PROVIDER: S-BSST2652 | biostudies-other |

REPOSITORIES: biostudies-other