FAQ

General Use

Can I analyze 2D data with VTEA?

Yes. VTEA supports 2D and 3D image processing, segmentation and mapping to the image volume. The segmentation methods provided in VTEA will operate on 2D images. It is recommended to use “Connect 2D/3D with kDTree.”

What is the upper limit of channels that VTEA can handle?

We have successfully tested VTEA on CODEX datasets with >40 channels. VTEA is limited only by what ImageJ/FIJI/Bioformats can load. Because VTEA relies on ImageJ/FIJI for image rendering, images with more than 7 channels can be difficult to visualize.

What is the largest image(filesize) VTEA can operate on?

VTEA is only limited by how much RAM it can use and the maximum size of a single frame that can be loaded by FIJI and/or the installed Java version. The development of more efficient image loading strategies to circumvent this limitation is a topic of ongoing development and is expected as early in version 1.5 and required for version 2.

Can I import a segmentation map from a different tool (StarDist, ilastik, CellPose etc.)?

Yes. This can be done by using the segmentation option, “Prelabelled Nuclei.”

Can I import features I’ve calculated in other tools (MorpholibJ, ilastik, etc.)?

Yes. This will be the subject of a future sketch.

Is there a long-term support plan for VTEA?

Yes. VTEA was first released five years ago in 2017 and is central to a number of research projects. Our intention is to continue to support and develop version 1 for the next 4-5 years for use in on-going funded projects. This will include addressing bugs, incremental additions to the existing framework (new segmentation, graph-based clustering and neighborhood analyses), expand the support for combined analysis (integration across and between imaging datasets) and explore new supervised analysis and visualization approaches. Developemment of VTEA 2.0 will begin soon with a focus on improving data handling under-the-hood (for support of Terabyte scale data) and implementing multimodal integration (from images to transcriptomics).

Is there a citation for VTEA?

Original publication, https://doi.org/10.1681/ASN.2016091027.

Manuscript for version 1.0 on Bioarchives: https://doi.org/10.1101/2021.12.27.474025.

Software release on Zenodo https://doi.org/10.5281/zenodo.5110084.

Do you have examples of VTEA use in publications?

  1. Lake BB, Menon R, Winfree S, et al. An Atlas of Healthy and Injured Cell States and Niches in the Human Kidney. Genomics; 2021. doi:10.1101/2021.07.28.454201
  2. Ferkowicz MJ, Winfree S, et al. for the Kidney Precision Medicine Project. Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline. Lab Invest. 2021;101(5):661-676. doi:10.1038/s41374-020-00518-w
  3. Black LM, Farrell ER, Barwinska D, et al. VEGFR3 tyrosine kinase inhibition aggravates cisplatin nephrotoxicity. Am J Physiol-Ren Physiol. 2021;321(6):F675-F688. doi:10.1152/ajprenal.00186.2021
  4. Black LM, Winfree S, Khochare SD, et al. Quantitative 3-dimensional imaging and tissue cytometry reveals lymphatic expansion in acute kidney injury. Lab Invest. 2021;101(9):1186-1196. doi:10.1038/s41374-021-00609-2
  5. Varberg KM, Winfree S, Chu C, et al. Kinetic analyses of vasculogenesis inform mechanistic studies. Am J Physiol-Cell Physiol. 2017;312(4):C446-C458. doi:10.1152/jpcell.00367.2016
  6. Makki MS, Winfree S, Lingeman JE, et al. A Precision Medicine Approach Uncovers a Unique Signature of Neutrophils in Patients With Brushite Kidney Stones. Kidney Int Rep. 2020;5(5):663-677. doi:10.1016/j.ekir.2020.02.1025
  7. Woloshuk A, Khochare S, Almulhim AF, et al. In Situ Classification of Cell Types in Human Kidney Tissue Using 3D Nuclear Staining. Cytometry A. 2021;99(7):707-721. doi:10.1002/cyto.a.24274

Segmentation and Morphology

Can I adjust the image processing to improve the segmentation?

Explorer windows and gating

Can I export images of my gated cells?