Datasets:

rjaditya
/

ImagesNepal

	This README.txt file was generated on 2024-09-15 by Pranav Shrestha

	--------------------
	GENERAL INFORMATION
	--------------------

	1. Title of Dataset: erythroSight: Open-access image dataset of blood cells from individuals with sickle cell disease and/or beta-thalassemia or without known hemaglobinopathies, captured using automated microscope Octopi

	2. Author Information
	A. Principal Investigator Contact Information
	Name: Dr. Boris Stoeber
	Institution: The University of British Columbia
	Email: boris.stoeber@ubc.ca

	B. Associate or Co-investigator Contact Information
	Name: Dr. Pranav Shrestha
	Institution: The University of British Columbia
	Email: pranav.shrestha@alumni.ubc.ca


	3. Date of data collection (single date, range, approximate date):

	2022-09 to 2023-03

	4. Geographic location of data collection:

	Mount Sagarmatha Polyclinic and Diagnostic Center, Nepalgunj, Nepal
	BC Children's Hospital, Vancouver, Canada
	St. Paul's Hospital, Vancouver, Canada

	5. Information about funding sources that supported the collection of the data:
	University of British Columbia Award Number: AWD-017004
	University of British Columbia Award Number: AWD-023617 VPHEALTH 2023
	Canada Research Chairs Award Number: CRC-2017-00041

	---------------------------
	SHARING/ACCESS INFORMATION
	---------------------------

	1. Licenses/restrictions placed on the data:

	These data are available under a CC BY 4.0 license <https://creativecommons.org/licenses/by/4.0/>

	2. Links to publications that cite or use the data:
	https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4908786
	https://www.sciencedirect.com/science/article/pii/S0006497123053946

	3. Links/relationships to ancillary data sets or software packages: N/A

	4. Was data derived from another source? No

	5. Recommended citation for this dataset: Pranav Shrestha, Hongquan Li, Manu Prakash, Hayley Merkeley, Videsh Kapoor, Rajan Pande, Boris Stoeber. (2024). erythroSight: Open-access image dataset of blood cells from individuals with sickle cell disease and/or beta-thalassemia or without known hemaglobinopathies, captured using automated microscope Octopi. Federated Research Data Repository. doi: 10.20383/103.0916


	---------------------
	DATA & FILE OVERVIEW
	---------------------

	1. High-level file structure
	Note: the detailed file structure is provided at the end of the document. The file structure for the images directories are also provided in attached file "FileStructureImages.png".

	erythroSight/
	├── ImagesCanada/
	│ ├── RAW/
	│ └── DPC/
	├── ImagesNepal/
	│ ├── RAW/
	│ └── DPC/
	├── CellSegmentation/
	│ └── models/
	│ └── OutlinesCanada/
	│ └── OutlinesNepal/
	├── MorphologicalParameters/
	│ ├── Canada/
	│ ├── Nepal/
	└── Plots/
	└── 1DCharacterization/


	2. Relationship between files, if important: All the images (raw left and right half images; processed DPC images) are in directories "ImagesCanada" and "ImagesNepal". The processed data are saved in directories "CellSegmentation" and "MorphologicalParameters". The plots for 1D characterization are saved "Plots".

	3. Additional related data collected that was not included in the current data package: Individual gold standard HPLC reports are not included, but the diagnosis or interpretation of the HPLC tests are saved as directory or file names, where "AA" or "N" = normal, "AS" or "SCT" = sickle cell trait, "SCD" = sickle cell disease; "ABeta" = Beta-thalassemia trait; "SS" = Homozygous sickle cell disease; "SBeta" = Sickle cell disease with beta-thalassemia.

	4. Are there multiple versions of the dataset? No


	---------------------------
	METHODOLOGICAL INFORMATION
	---------------------------

	1. Description of methods used for collection/generation of data:

	Blood samples were collected from healthy volunteers (HbAA) and participants with known hemoglobinopathies (HbA/β-thalassemia, HbAS, HbS/β-thalassemia, HbSS). The performance of six low-cost tests (Conventional sickling test; HbS solubility test; HemoTypeSC; Sickle SCAN; Gazelle Hb variant test; Automated sickling test using automated microscopy and machine learning) was evaluated against HPLC; ClinicalTrials.gov Identifier: NCT05506358.

	2. Methods for processing the data:

	Raw images from the Octopi microscope of the sickling test were processed to create differential phase contrast images. After cell segmentation using Cellpose 2.0, morphological parameters were calculated using ImageJ, and plotted using MATLAB.


	3. Instrument- or software-specific information needed to interpret the data:

	Instrument used to collect data: Octopi microscope from Prakash Lab at Stanford University
	Software and programming languages used for processing data: Python, MATLAB, ImageJ. All programs/code are provided in Github: https://github.com/p-shrestha/erythroSight

	4. Standards and calibration information, if appropriate: N/A

	5. Environmental/experimental conditions: Experiments were performed at room temperature (between 20°C-25°C). Some samples were incubated at 37°C.

	6. Describe any quality-assurance procedures performed on the data: Collected data was analyzed during imaging, and processed data were analyzed for manuscript reporting.

	7. People involved with sample collection, processing, analysis and/or submission: People involved are listed as authors or in acknowledgements in publications.


	-----------------------------------------------------------------
	DETAILED FILE STRUCTURE
	-----------------------------------------------------------------

	ImagesCanada/ (or ImagesNepal/)
	├── RAW/
	│ ├── N-001/
	│ │ ├── t0/
	│ │ └── t02hrs/
	│ │ ├── Ai_.../
	│ │ │ ├── 0/
	│ │ │ │ ├── 0_0_0_BF_LED_matrix_left_half.bmp
	│ │ │ │ ├── 0_0_0_BF_LED_matrix_right_half.bmp
	│ │ │ │ ├── 0_1_0_BF_LED_matrix_left_half.bmp
	│ │ │ │ ├── 0_1_0_BF_LED_matrix_right_half.bmp
	│ │ │ │ └── ...
	│ │ │ │ └── .csv
	│ │ │ ├── acquisition parameters.json
	│ │ │ └── configurations.xml
	│ │ └── Aii_.../
	│ ├── N-002/
	│ ├── N-003/
	│ └── ...
	│ ├── SCT-009/
	│ ├── TimeSeries/
	│ │ ├── SCD-001/
	│ │ └── SCD-004/
	│ │ └── ...
	│ └── RatioStudy/
	│ └── N-005/
	└── DPC/
	├── N-001/
	│ ├── t0/
	│ └── t02hrs/
	│ ├── Ai_.../
	│ │ ├── N-001_t02hrs_Ai_0_0_0_DPC.png
	│ │ ├── N-001_t02hrs_Ai_0_1_0_DPC.png
	│ │ └── ...
	│ └── Aii_.../
	├── N-002/
	├── N-003/
	└── ...
	├── TimeSeries/
	│ ├── SCD-001/
	│ └── SCD-004/
	│ └── ...
	└── RatioStudy/
	└── N-005/

	CellSegmentation/
	├── models
	│ ├── Other
	│ └── sickle20230404
	├── OutlinesCanada
	│ ├── N-001
	│ │ ├── t0
	│ │ └── t02hrs
	│ │ ├── Ai_.../
	│ │ │ ├── N-001_t02hrs_Ai_0_0_0_DPC_cp_outlines.txt
	│ │ │ ├── N-001_t02hrs_Ai_0_1_0_DPC_cp_outlines.txt
	│ │ │ └── ...
	│ │ └── Aii_.../
	│ ├── N-002
	│ ├── N-003
	│ └── ...
	└── OutlinesNepal
	├── AA-001
	├── AA-002
	└── ...


	MorphologicalParameters/
	├── Canada/
	│ ├── N-001_MorphologicalParameters.tar**
	│ ├── N-002_MorphologicalParameters.tar
	│ └── ...
	└── Nepal/
	├── AA-001_MorphologicalParameters.tar
	├── AA-002_MorphologicalParameters.tar
	└── ...

	** The tar files have nested directories where the final files are .csv files storing the morphological parameter information of each cell

	Plots
	└── 1DCharacterization
	├── t02hrs
	│ └── cnCombined
	│ └── 30b40mp
	│ ├── AA
	│ │ ├── generalinfo.mat
	│ │ ├── histData.mat
	│ │ └── morphParamData.mat
	│ ├── ABeta
	│ │ ├── generalinfo.mat
	│ │ ├── histData.mat
	│ │ └── morphParamData.mat
	│ ├── AS
	│ │ ├── generalinfo.mat
	│ │ ├── histData.mat
	│ │ └── morphParamData.mat
	│ ├── Figures***
	│ └── SCD
	│ ├── generalinfo.mat
	│ ├── histData.mat
	│ └── morphParamData.mat
	└── TimeSeries
	├── SCD-001
	│ ├── Ai…
	│ │ └── Figures***
	│ ├── generalinfo.mat
	│ ├── histData.mat
	│ └── morphParamData.mat
	├── SCD-004
	└── …

	*** Figures directory contains .fig and .png files for plots