{"cells":[{"metadata":{},"cell_type":"markdown","source":""},{"metadata":{},"cell_type":"markdown","source":"As a pathology resident with skills in nephropathology, it was impossible for me to miss out this competition !
\n\nNephropathology is a vast, beautiful but complicated discipline concerning the study of kidney disease.\nLupus, diabetes, amyloidosis... Many systemic diseases have renal expression which generally lead to end-stage renal disease and requires dialysis. To initiate therapy, a rapid diagnosis of these disease must be made and the gold standard stay the histopathological examination of kidney sample.
\nThey can be obtained in several ways : by biopsy where the fragment is a long core of several millimeters or a surgical sample, as is the case in this competition.
\n\nThe objective of this competition lies in the detection of glomeruli, the main structure composing the nephron. Therefore, it's important to understand its structure and distribution in the renal parenchyma : they're not randomly placed !
\n\nHere is the first notebook of a series of 3, listing medical knowledge useful for the detection of glomerulus. This notebook will be theorical but essential to understand the following. It will deal with the anatomy and histology of the normal kidney, nephron and finally glomerulus. The second one will deal with the different possible architectures of the glomerulus according to the stage of maturation or pathological injury and finally the third one will deal with the existing correlations between glomerular architecture and patient data. All of them will allow you to better apprehend their detection and thus increase your performance !\n\nIf you find this notebook useful, don't hesitate to upvote it to encourage me to write the following quickly !\n\nGood luck to all !"},{"metadata":{},"cell_type":"markdown","source":"1. [Kidney anatomy](#1)\n2. [Nephron anatomy](#2)\n3. [Glomerulus anatomy](#3)\n4. [Glomerulus histology](#4)\n"},{"metadata":{},"cell_type":"markdown","source":"1. Kidney anatomy
"},{"metadata":{},"cell_type":"markdown","source":""},{"metadata":{},"cell_type":"markdown","source":"The kidney is the first organ of the urinary tract. It's located on the left and right retroperitoneal space and measures about 12 cm long in human adults.\nIt has multiple functions, such as hormonal homeostasis, regulation of blood pressure, but above all, the production of urine by filtering the circulating blood, allowing the elimination of toxins.
\nEvery day, 172 liters of primary urine are produced by kidneys and 99% of this urine will be reabsorbed by the nephrons, resulting in the excretion of 1.5 liters of urine per day in the average adult.
\nThe blood arrives by the renal artery which will divide itself into renal arterioles, then capillaries where the blood will be filtered, then join the renal venules and finally the renal vein.
\nAs you can see on the scheme, this anastomosis between the arterial and venous circulation is done in the cortex, the external part of the kidney : it's in this area that glomeruli will be found !"},{"metadata":{},"cell_type":"markdown","source":"2. Nephron anatomy
"},{"metadata":{},"cell_type":"markdown","source":""},{"metadata":{},"cell_type":"markdown","source":"Each normal kidney has an average of 1,000,000 nephrons. It is the microscopic structural and functional unit of the kidney, composed of a renal corpuscule and a renal tubule. The renal corpuscule consist of an aggregate of capillaries which form the glomerulus with its Bowman's capsule. The renal tubules starts after the Bowman's capsule and are made of 5 anatomically and functionnaly different parts : the proximal tubule (in blue), the loop of Henle, the distal tubule (in green), the junctional tubule (in orange) and finally the collecting tubule (in orange) : all of them are dedicated to urine production and reabsorption."},{"metadata":{},"cell_type":"markdown","source":"3. Glomerulus anatomy
"},{"metadata":{},"cell_type":"markdown","source":""},{"metadata":{},"cell_type":"markdown","source":"The best way to understand how a glomerulus works is to follow the path of the blood which will then become urine. As shown in this scheme, the blood arrives through the associated afferent arteriole. It's then filtered through the wall of these capillaries, between the endothelial cells, thanks to hydrostatic pressure differentials. On the other side of the basal membrane are the podocytes with long foot processes called pedicels. Once these 3 layers have passed, the blood ends up in Bowman's space and constitutes the primitive urine. It will then be drained into the renal tubule starting with its proximal portion.
\nIt's this whole set, called the glomerulus, that will have to be detected and differentiated from the rest of the adjacent renal parenchyma and the best way to do this is to understand what it looks like on a histological level."},{"metadata":{},"cell_type":"markdown","source":"4. Glomerulus histology
"},{"metadata":{},"cell_type":"markdown","source":""},{"metadata":{},"cell_type":"markdown","source":"Here is a screen of a glomerulus from HuBMAP's data set. As said before, we are located in the renal cortex so only the glomeruli, the proximal and the distal tubule sections are visible.
\nThe distinction between these tubes is not always easy. In general, the proximal portions have lighter nuclei with brush borders at the apical pole, which appear purple while the distal portions have darker nuclei, and do not have these brush borders, making the tube lumen more visible (white portion in the center of the tube).
\nYou now know how to recognize a normal glomerulus, so the next step will be to recognize the pathological glomeruli which are very numerous within the dataset, and it's not always easy !\n\nGood luck !\n\n\n"}],"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"pygments_lexer":"ipython3","nbconvert_exporter":"python","version":"3.6.4","file_extension":".py","codemirror_mode":{"name":"ipython","version":3},"name":"python","mimetype":"text/x-python"}},"nbformat":4,"nbformat_minor":4}