Skip to main content

LUP Student Papers

LUND UNIVERSITY LIBRARIES

Particle Detection in Bone Marrow Using CNNs and Transformer Networks

Källén, Anna LU and Williams, Marcus LU (2023) In Master's Theses in Mathematical Sciences FMAM05 20231
Mathematics (Faculty of Engineering)
Abstract (Swedish)
The critical role of hematological stem cells, concentrated in bone marrow, in disease diagnosis makes the detection of these cells an imperative task. The current process, however, is slow and heavily reliant on expert interpretation, underscoring the need for automation. In this thesis, we collected a 20x microscopy dataset of real and fake bone marrow particles and fine-tuned several CNNs and Transformer networks on the task of classifying them. We performed a hyperparameter investigation, explored whether illuminating the sample from an angle improves performance and analysed what the networks are looking for with several interpretability methods.

The best results were obtained by fine-tuning a Swin Transformer V2S, using images... (More)
The critical role of hematological stem cells, concentrated in bone marrow, in disease diagnosis makes the detection of these cells an imperative task. The current process, however, is slow and heavily reliant on expert interpretation, underscoring the need for automation. In this thesis, we collected a 20x microscopy dataset of real and fake bone marrow particles and fine-tuned several CNNs and Transformer networks on the task of classifying them. We performed a hyperparameter investigation, explored whether illuminating the sample from an angle improves performance and analysed what the networks are looking for with several interpretability methods.

The best results were obtained by fine-tuning a Swin Transformer V2S, using images captured standard illumination settings. This model reached 97.19% on the test set. Different hyperparameters were evaluated with the result that most hyperparameters are of little significance, apart from dataset size where the accuracy increased logarithmically with the dataset size. A much faster model was made by quantising ResNet18 to 8-bits, which had an accuracy of 96.75% while only taking 59ms per image for inference on microscope hardware, making it feasible to use in an automated bone marrow examination process in the future. (Less)
Please use this url to cite or link to this publication:
author
Källén, Anna LU and Williams, Marcus LU
supervisor
organization
course
FMAM05 20231
year
type
H2 - Master's Degree (Two Years)
subject
keywords
Bone Marrow, Dark Field Microscopy, Fourier Ptychography, Machine Learning, Convolutional Neural Networks, Transformer Networks, Quantisation
publication/series
Master's Theses in Mathematical Sciences
report number
LUTFMA-3498-2023
ISSN
1404-6342
other publication id
2023:E17
language
English
id
9121961
date added to LUP
2023-08-22 17:31:16
date last changed
2023-08-22 17:31:16
@misc{9121961,
  abstract     = {{The critical role of hematological stem cells, concentrated in bone marrow, in disease diagnosis makes the detection of these cells an imperative task. The current process, however, is slow and heavily reliant on expert interpretation, underscoring the need for automation. In this thesis, we collected a 20x microscopy dataset of real and fake bone marrow particles and fine-tuned several CNNs and Transformer networks on the task of classifying them. We performed a hyperparameter investigation, explored whether illuminating the sample from an angle improves performance and analysed what the networks are looking for with several interpretability methods.

The best results were obtained by fine-tuning a Swin Transformer V2S, using images captured standard illumination settings. This model reached 97.19% on the test set. Different hyperparameters were evaluated with the result that most hyperparameters are of little significance, apart from dataset size where the accuracy increased logarithmically with the dataset size. A much faster model was made by quantising ResNet18 to 8-bits, which had an accuracy of 96.75% while only taking 59ms per image for inference on microscope hardware, making it feasible to use in an automated bone marrow examination process in the future.}},
  author       = {{Källén, Anna and Williams, Marcus}},
  issn         = {{1404-6342}},
  language     = {{eng}},
  note         = {{Student Paper}},
  series       = {{Master's Theses in Mathematical Sciences}},
  title        = {{Particle Detection in Bone Marrow Using CNNs and Transformer Networks}},
  year         = {{2023}},
}