The composition of the tumour microenvironment in follicular lymphoma (FL) is a relevant factor in determining disease progression and treatment response. This dataset is a collection of 349 FL diagnostic tissue micro-array (TMA) cores from 130 patients, stained using multi-plex immunofluorescence for: • CD4+ cells • Cytotoxic T cells (CD8+) • T regulatory cells (Tregs [CD4+FOXP3+]) • Macrophages (CD68+) • PD1+ lymphocytes • B cells/follicular dendritic cells (CD21+) • DAPI (4′,6-diamidino-2-phenylindole) nuclear counterstain Changes from previous version 2 ---------- - Raw .im3 image files provided - Spectral library images provided - Labels of nuclear annotations in 16bit format Cohort -------- FL patients according to the WHO 2008 classification were identified from the archives of The Christie NHS Foundation Trust, Manchester, UK. The study was conducted with approval by the North-West Multi-centre Ethics Committee (03/08/016) and according to the Declaration of Helsinki. Examination of the records of 350 FL patients in a random order identified 262 patients meeting the inclusion criteria: adult patients with previously untreated FL; diagnosed from incisional or excisional biopsy; and treated at first presentation with radiotherapy, watchful waiting or a combination of chemotherapy and rituximab immunotherapy. Pre-treatment biopsies were requested for 262 patients, of which 130 had sufficient tissue for analysis. A histological diagnosis of FL was confirmed by an expert haemato-pathologist (R.B). Note: Three patients (FL_59, FL_106 and FL_129) have grade 3b, which is considered equivalent to Diffuse Large B-cell lymphoma. Image format and software compatibility --------------------------------------------- Each image represents a single TMA core as a .im3 raw multispectral image format, containing the following spectra: • DAPI (nuclear) • 650 fluorophore signal for CD68 marker (membrane) • 570 fluorophore signal for CD21 marker (membrane) • 540 fluorophore signal for CD8 marker (membrane) • 690 fluorophore signal for PD1 marker (membrane) • 620 fluorophore signal for CD4 marker (membrane) • 520 fluorophore signal for FOXP3 (nuclear) • Auto-fluorescence The commercial software inForm 2.4 (Akoya Biosciences) is compatible with this format. The images can be unmixed with inForm software by using the spectral library provided. Annotations ------------- Annotations are provided for nuclear segmentation. In a set of 41 small patches the outlines have been drawn manually for 69780 nuclei. A patch from the DAPI channel and corresponding label are given as .tif images. Data structure ---------------- The data is split across multiple different datasets, all referenced below. They include: • FL_0-129 zip files: Raw images for 130 patients, each zip file a single patient. • nuclear_segmentation_annotations.zip: The nuclear segmentation annotations. • spectral library.zip: The raw images used to build the spectral library with inForm software
