PECAn, a pipeline for image processing and statistical analysis of complex mosaic 3D tissues
Baumgartner, M. E.; Langton, P. F.; Mastrogiannopoulos, A.; Logeay, R.; Piddini, E.
Show abstract
Investigating organ biology requires sophisticated methodologies to induce genetically distinct clones within a tissue. Microscopic analysis of such samples produces information-rich 3D images. However, the 3D nature and spatial anisotropy of clones makes sample analysis challenging and slow and limits the amount of information that can be extracted manually. Here we have developed a pipeline for image processing and statistical data analysis which automatically extracts sophisticated parameters from complex multi-genotype 3D images. The pipeline includes data handling, machine-learning-enabled segmentation, multivariant statistical analysis, and graph generation. This enables researchers to run rigorous analyses on images and videos at scale and in a fraction of the time, without requiring programming skills. We demonstrate the power of this pipeline by applying it to the study of Minute cell competition. We find an unappreciated sexual dimorphism in Minute competition and identify, by statistical regression analysis, tissue parameters that model and predict competitive death.
Matching journals
The top 8 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- The replicative helicase CMG is required for the divergence of cell fates during asymmetric cell division in vivo 95%
- The ubiquitin ligase Hecw controls oogenesis and neuronal homeostasis by promoting the liquid state of ribonucleoprotein particles 94%
- The deubiquitylating enzyme Fat Facets promotes Fat signalling and restricts tissue growth 94%
Similar papers in this journal
Similar papers in this journal
- Exploring endocytic compartment morphology with systematic genetics and single cell image analysis 94%
- KDML: a machine-learning framework for inference of multi-scale gene functions from genetic perturbation screens 93%
- Vesalius: high-resolution in silico anatomization of Spatial Transcriptomic data using Image Analysis 93%
Similar papers in this journal
- The level of oncogenic Ras controls the malignant transformation of Lkb1 mutant tissue in vivo. 95%
- smiFISH and embryo segmentation for single-cell multi-gene RNA quantification in arthropods 94%
- Nance-Horan-Syndrome-like 1b controls mesodermal cell migration by regulating protrusion and actin dynamics during zebrafish gastrulation. 93%
Similar papers in this journal
- Combined inactivation of RB and Hippo pathways converts differentiating photoreceptors into eye progenitor cells through derepression of homothorax 95%
- Tissue mechanics and systemic signaling safeguard epithelial tissue against spindle misorientation. 94%
- Microtubules coordinate mitochondria transport with myofibril morphogenesis during muscle development 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.