Tumour Infiltrating Lymphocytes in Follicular Lymphoma - additional data

Dataset

Description

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
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- Raw .im3 image files provided
- Spectral library images provided
- Labels of nuclear annotations in 16bit format

Cohort
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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
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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
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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
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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.
Date made available4 Jan 2021
PublisherMendeley Data

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