DeepCIS: An end-to-end Pipeline for Cell-type aware Instance Segmentation in Microscopic Images. - Nabeel Khalid; Mohsin Munir; Christoffer Edlund; Timothy R. Jackson; Johan Trygg; Rickard Sjögren; Andreas Dengel 001; Sheraz Ahmed (BHI, 2021)

DeepCeNS: An end-to-end Pipeline for Cell and Nucleus Segmentation in Microscopic Images. - Nabeel Khalid; Mohsin Munir; Christoffer Edlund; Timothy R. Jackson; Johan Trygg; Rickard Sjögren; Andreas Dengel 001; Sheraz Ahmed (IJCNN, 2021)

DeepMuCS: A Framework for Co-culture Microscopic Image Analysis: From Generation to Segmentation. - Nabeel Khalid; Mohammadmahdi Koochali; Vikas Rajashekar; Mohsin Munir; Christoffer Edlund; Timothy R. Jackson; Johan Trygg; Rickard Sjögren; Andreas Dengel 001; Sheraz Ahmed (BHI, 2022)

Point2Mask: A Weakly Supervised Approach for Cell Segmentation Using Point Annotation. - Nabeel Khalid; Fabian Schmeisser; Mohammadmahdi Koochali; Mohsin Munir; Christoffer Edlund; Timothy R. Jackson; Johan Trygg; Rickard Sjögren; Andreas Dengel 001; Sheraz Ahmed (MIUA, 2022)

PACE: Point Annotation-Based Cell Segmentation for Efficient Microscopic Image Analysis. - Nabeel Khalid; Tiago Comassetto Fróes; Maria Caroprese; Gillian Lovell; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (ICANN (2), 2023)

CellSpot: Deep Learning-Based Efficient Cell Center Detection in Microscopic Images. - Nabeel Khalid; Maria Caroprese; Gillian Lovell; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (ICANN (8), 2024)

Bounding Box Is All You Need: Learning to Segment Cells in 2D Microscopic Images via Box Annotations. - Nabeel Khalid; Maria Caroprese; Gillian Lovell; Daniel A. Porto; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (MIUA (1), 2024)

CellGenie: An End-to-End Pipeline for Synthetic Cellular Data Generation and Segmentation: A Use Case for Cell Segmentation in Microscopic Images. - Nabeel Khalid; Mohammadmahdi Koochali; Duway Nicolas Lesmes-Leon; Maria Caroprese; Gillian Lovell; Daniel A. Porto; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (MIUA (1), 2024)

SAT: Segment and Track Anything for Microscopy. - Nabeel Khalid; Mohammadmahdi Koochali; Khola Naseem; Maria Caroprese; Gillian Lovell; Daniel A. Porto; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (ICAART (2), 2025)

YeastFormer: An End-to-End Instance Segmentation Approach for Yeast Cells in Microstructure Environment. - Khola Naseem; Nabeel Khalid; Lea Bertgen; Johannes M. Herrmann; Andreas Dengel 001; Sheraz Ahmed (ICAART (2), 2025)