Biography

Fakrul Islam tushar is a Medical Imaging & Computer Vision Engineer, primarily engaged in research, computer-aided diagnosis and healthcare innovation using machine learning, neural networks, and image analysis driven solutions. He graduated from the Erasmus+ Joint Master in Medical Imaging and Applications and is currently a Post-Graduate Research Associate at the Carl E. Ravin Advanced Imaging Laboratories (RAI Labs), Duke University Medical Center, USA. He earned a Bachelor of Science degree in Electrical and Electronics Engineering at American International University Bangladesh (AIUB). He is a recipient of the “Cum Laude” distinction and academic honor at the 17th Convocation Ceremony of AIUB, “Dean’s Award” for his final-year undergraduate research project, the European Union: Erasmus+ Grant and the Duke University: Masters Thesis Grant. His past affiliations include IEEE AIUB Student Branch, Teach For Bangladesh and “Literacy Through Leadership”.

Interests

  • Artificial Intelligence
  • Medical Image Processing and Analysis
  • Image Segmentation
  • Deeplearning
  • NLP

Education

  • Associate in Research, 2019-present

    Duke University Medical Center

  • Masters in Medical Imaging and Applications, 2017-2019

    Erasmus Mundus Joint Master ( University of Burgundy; University of Cassino; University of Girona, Duke University)

  • BSc in Electrical & Electronic Engineering, 2013-2017

    American International University Bangladesh

Journals & Conferences

(2018). Development of a Modular Biopotential Amplifier Trainer for Biomedical Instrumentation Laboratory Experiments. Science Journal of Circuits, Systems and Signal Processing. Vol. 7, No. 2, 2018, pp. 48-59.

PDF Code Poster DOI Slides

(2019). Classification of Chest CT Using Case-level Weak Supervision. Proc. SPIE 10950, Medical Imaging 2019: Computer-Aided Diagnosis, 1095017 (13 March 2019).

PDF Code Video DOI Slides

(2019). Brain Tissue Segmentation Using NeuroNet With Different Pre-processing Techniques. 2019 Joint 8th International Conference on Informatics, Electronics & Vision (ICIEV) and 2019 3rd International Conference on Imaging, Vision & Pattern Recognition (icIVPR), Spokane, WA, USA, 2019, pp. 223-227.

PDF Code DOI Pre-print Slides

(2020). Weakly supervised 3D classification of chest CT using aggregated multi-resolution deep segmentation features. Proc. SPIE 11314, Medical Imaging 2020: Computer-Aided Diagnosis, 1131408.

PDF Code Video DOI Slides

(2020). Attention-guided classification of abnormalities in semi-structured computed tomography reports. Proc. SPIE 11314, Medical Imaging 2020: Computer-Aided Diagnosis, 113141P.

PDF Video DOI Slides

(2020). DSNet: Automatic dermoscopic skin lesion segmentation. Computers in Biology and Medicine,Volume 120,2020,103738,ISSN 0010-4825..

Code DOI

Projects

Brain Tissue Segmentation Using NeuroNet With Different Pre-processing Techniques

Automatic segmentation of brain Magnetic Resonance Imaging (MRI) images is one of the vital steps for quantitative analysis of brain for further inspection. In this paper, NeuroNet has been adopted to segment the brain tissues (white matter (WM), grey matter (GM) and cerebrospinal fluid (CSF)) which uses Residual Network (ResNet) in encoder and Fully Convolution Network (FCN) in the decoder. To achieve the best performance, various hyper-parameters have been tuned, while, network parameters (kernel and bias) were initialized using the NeuroNet pre-trained model. Different pre-processing pipelines have also been introduced to get a robust trained model. The model has been trained and tested on IBSR18 data-set. To validate the research outcome, performance was measured quantitatively using Dice Similarity Coefficient (DSC) and is reported on average as 0.84 for CSF, 0.94 for GM, and 0.94 for WM. The outcome of the research indicates that for the IBSR18 data-set, pre-processing and proper tuning of hyper-parameters for NeuroNet model have improvement in DSC for the brain tissue segmentation.

Brain Tissue Segmentation Using Expectation Maximization (EM)

The segmentation is an essential part of many computer vision systems and medical applications. The goal is to divide an input image into a set of non-overlapping regions which union is the entire image. The Expectation-Maximization (EM) algorithm is an iterative technique designed for probabilistic models. Expectation-Maximization algorithm for segmenting brain MRI images (T1-w image) into the three main tissues: white matter (WM), grey matter (GM) and cerebrospinal fluid (CSF).

Skin Lesion classification

The idea of the project is to apply 2D U-net to Segment the RIO using the publicly available data from ISIC Challenge 2017 and classification of the segmented region for classification of lesion. Multiple OTS model ( Resnet, VGG, Densenet) were used for classification. Among the model VGG out performed all other model. Ensembling of the models was also applied and performed better than single classifier, Democracy always wins.

Lung Disease Classification with 2D Multi-channel effect analysis

Lung diseases classification in 2D using chest CT cases and Analysis the multi-channel effect on classification. This work is been done during summer internship July-Aguest 2018, Duke University Medical Center.

Registration as Data-Augumentation for CT

Main idea of this project was making some new data using simple registration technique from existing CT data. This code be a possible alternative of arbitrary augmentation such as flip, rotation, zoom etc. A simple but powerful non-rigid registration technique BSpline is been used for this. There are number of parameters that can be used to make the variation of the registration to make new data which is completely different from Moving and Fixed CT used for registration.

Automatic Skin Lesion Segmentation Using GrabCut in HSV Colour Space

Skin lesion segmentation is one of the first steps towards automatic Computer-Aided Diagnosis of skin cancer. Vast variety in the appearance of the skin lesion makes this task very challenging. The contribution of this paper is to apply a power foreground extraction technique called GrabCut for automatic skin lesion segmentation with minimal human interaction in HSV color space. Preprocessing was performed for removing the outer black border. Jaccard Index was measured to evaluate the performance of the segmentation method. On average, 0.71 Jaccard Index was achieved on 1000 images from ISIC challenge 2017 Training Dataset.

Cyclical Learning Rates for Training Neural Networks With Unbalanced Data Sets

s the learning rate is one of the most importanthyper-parameters to tune for training convolutional neural net-works. In this paper, a powerful technique to select a range oflearning rates for a neural network that named cyclical learningrate was implemented with two different skewness degrees. Itis an approach to adjust where the value is cycled between alower bound and upper bound. CLR policies are computationallysimpler and can avoid the computational expense of fine tuningwith fixed learning rate. It is clearly shown that changing thelearning rate during the training phase provides by far betterresults than fixed values with similar or even smaller number of epochs.

Mass Detection in Breast Using Transfer Learning for Computer Aided Diagnosis

Mammography is the most widely used gold standard method for the screening of the breast cancer and Mass detection is the prominent pre-processing step. State-of-art performances of the DCNN architectures in the field of classification made them an obvious choice for the image classifications. However, due to limited availability of medical data, application of DCNN architectures in medical images is challenging. In this project our contribution was mass detection in mammographic images using two different approaches. First approach was applying transfer learning concept which lessen the demand of data to use a pre-trained publicly available VGG16 model and second approach was training a Alexnet from the scratch to classify mass and non-mass mammographic images. Both the models were trained and tested with different hyperparameters and different data size. From the experiment results, it can be concluded that transfer learning approach for VGG16, training from fully connected layer 2 (fc2) has promising expected result for mass detection. In our research, maximum accuracy for mass detection was 93.60% for VGG16 with 13500 train images.

Design an inverse kinematic controller to move end-effector

Design an inverse kinematic controller to move end-effector. This work is done as a coursework for the 2nd semester of MAIA in Introduction to Robotics course.The task was to design an Inverse Kinematic controller to move the end-effector from the position pA to the position pB The movement should be repeated 3 times by control: 1)the position-only without exploiting the redundancy 2)the position and the orientation without exploiting the redundancy (desired orientation equal to the initial one) 3)the position and the orientation avoiding an obstacle put in p0 (desired orientation equal to the initial one)

Quantification of Trabeculae Inside the Heart from MRI Using Fractal Analysis

Left ventricular non-compaction (LVNC) is a rare cardiomyopathy (CMP) that should be considered as a possible diagnosis because of its potential complications which are heart failure, ventricular arrhythmias, and embolic events. For analysis cardiac functionality, extracting information from the Left ventricular (LV) is already a broad field of Medical Imaging. Different algorithms and strategies ranging that is semiautomated or automated has already been developed to get useful information from such a critical structure of heart. Trabeculae in the heart undergoes difference changes like solid from spongy. Due to failure of this process left ventricle non-compaction occurred. In this project, we will demonstrate the fractal dimension (FD) and manual segmentation of the Magnetic Resonance Imaging (MRI) of the heart that quantify amount of trabeculae inside the heart. The greater the value of fractal dimension inside the heart indicates the greater complex pattern of the trabeculae in the heart.

Development of a Modular Biopotential Amplifier Trainer for Biomedical Instrumentation Laboratory Experiments

The availability of sophisticated source attribution techniques raises new concerns about privacy and anonymity of photographers, activists, and human right defenders who need to stay anonymous while spreading their images and videos. An image can be considered to be a combination of both significant (foreground) objects and some less significant (background) objects. Content aware image resizing (CAIR) algorithm uses the different edge detection methods to segregate the useful objects from the background. When applied to an image, CAIR can resize the image to a very different aspect ratio without destroying the aspect ratio of the useful objects in the image. In this project, we simply implement a content aware image resizing (CAIR) in MATLAB environment. The main idea to implement CAIR is to remove or insert the vertical or horizontal seams (paths of pixel) having the lowest energy. After implanted the Seam Carving Algorithm for Content aware image resizing (CAIR), analysis shows that the implemented seam carving for CAIR can generate more desirable resized images than cropping, resampling, and conventional seam carving techniques.

Face Recognition using Principal Component Analysis

Few years back, face recognition is only limited to personal identification, now this technology is been grown in the field of security, healthcare, personalized services etc. Many methods are developed to perform for face recognition and they work quit well.The basic idea of this project it to compute a data set of features from the face images 𝐼𝑞which have compared with a set of database images 𝐼1………𝐼𝑞 to detect the best match. Every pixel can be considered as a variable that means the dimensional space is very high. PCA is been used to decreasing the dimensionality of the image for making this recognition problem easier.

Development of a Modular Biopotential Amplifier Trainer for Biomedical Instrumentation Laboratory Experiments

This paper presents the design, development and implementation of a reconfigurable low-cost biopotential amplifier trainer module (RTR module) and quantitative analysis of the students’ compatibility with the trainer module. The trainer module can measure Electrocardiogram (ECG), Electroencephalogram (EEG) and Electromyogram (EMG) biopotential signals by reconfiguring the module using the basic circuit and filtering blocks. Given hand on experience, the module is designed and implemented in such reconfigurable manner that the students can avoid, disconnect and add any filtering blocks to understand the effect of these filters to the biopotential signals. The laboratory experience is an important component of the learning process. The RTR module is a low cost and compact educational tool. With this RTR module, the students should be able to recognize the biopotential signals and the acquisition methods in an intuitive and easy way, allowing them to improve their skills of designing biomedical instrumentation.

ASHA -A Solution to Help Autism

The name of our Application is ASHA Which mean Hope in Bengali. Here ASHA Stands for A Solution to Help Autism. The Idea of our App ASHA is to introduce a detection or test procedure for Autism.Autism is a spectrum of closely related disorders with a shared core of symptoms. Autism spectrum disorders appear in infancy and early childhood, causing delays in many basic areas of development, such as learning to talk, play, and interact with others.

Posts

3D Data-Augmentation Using tf.data and Volumentations-3D Library

In this blog, I will introduce a Library for 3D augmentations called volumentations-3D. .

3D Medical Imaging Pre-processing All-you-need

Pre-processing for 3D Medical Imaging.

Eramus Mundus Scholarship FAQs

Trying cover the FAQs abour ERASMUS+ Scholarship funed By European Union.

My Erasmus Experience-MAIA

Education with Travel & Cultural Experience.

Writing A Scholarship-Awarding Motivation Letter

A guide to writing a MOL/SOP.

Accomplish­ments

Cum Laude Distinction

Academic Honor for Academic Excellences at AIUB’s 17th Convocation.
See certificate

DEAN’S Award

For Undergrad final year project, securing 2nd place among 180 groups in Academic year 2016 and 2017.
See certificate

Academic Scholarship from American International University Bangladesh (AIUB)

For exceptional performance throughout the academic years (450,000 BDT)

Certifications

AI for Medical Diagnosis

See certificate

Neural Networks and Deep Learning

See certificate

Co-curricular Experience

 
 
 
 
 
 
 
 
 
 

Vice Chair

IEEE Microwave Theory and Techniques Society AIUB SB Chapter

Feb 2016 – Feb 2017 Dhaka
  • Planned events to Build interest in microwave related researches.
  • Successfully organized 3 workshops and 1 seminar on microwave related fields.
 
 
 
 
 

Vice Chair

IEEE Industry Application Society AIUB SB Chapter

Feb 2016 – Feb 2017 Dhaka
  • Collaborated with industries and organized 4 industrial tours for students.
  • Organized 4 workshops on stem fields, such as MATLAB, Building wiring, Arduino, and PCB fabrication.
  • Awarded “Exemplary New IAS Student Chapter 2016”
 
 
 
 
 

Youth Leader (Teacher)

Literacy Through Leadership (LTL)

Jan 2016 – Mar 2016 Dhaka
In collaboration with Teach For Bangladesh, contributed total 78 hours in 13 weeks’ period, 6 hours per week to improve 40 underprivileged Primary School students’ English Reading and writing skill.
 
 
 
 
 

IEEE Day Section Ambassador 2015 & 2016

IEEE

Jan 2016 – Dec 2017 Dhaka

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