Immunocto: a massive immune cell database auto-generated for histopathology
CoRR(2024)
Abstract
With the advent of novel cancer treatment options such as immunotherapy,
studying the tumour immune micro-environment is crucial to inform on prognosis
and understand response to therapeutic agents. A key approach to characterising
the tumour immune micro-environment may be through combining (1) digitised
microscopic high-resolution optical images of hematoxylin and eosin (H E)
stained tissue sections obtained in routine histopathology examinations with
(2) automated immune cell detection and classification methods. However,
current individual immune cell classification models for digital pathology
present relatively poor performance. This is mainly due to the limited size of
currently available datasets of individual immune cells, a consequence of the
time-consuming and difficult problem of manually annotating immune cells on
digitised H E whole slide images. In that context, we introduce Immunocto, a
massive, multi-million automatically generated database of 6,848,454 human
cells, including 2,282,818 immune cells distributed across 4 subtypes: CD4^+
T cell lymphocytes, CD8^+ T cell lymphocytes, B cell lymphocytes, and
macrophages. For each cell, we provide a 64×64 pixels H E image at
40× magnification, along with a binary mask of the nucleus and
a label. To create Immunocto, we combined open-source models and data to
automatically generate the majority of contours and labels. The cells are
obtained from a matched H E and immunofluorescence colorectal dataset from the
Orion platform, while contours are obtained using the Segment Anything Model. A
classifier trained on H E images from Immunocto produces an average F1 score of
0.74 to differentiate the 4 immune cell subtypes and other cells. Immunocto can
be downloaded at: https://zenodo.org/uploads/11073373.
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