Algorithms for Biological Cell Storing.

Date of Submission

December 2010

Date of Award

Winter 12-12-2011

Institute Name (Publisher)

Indian Statistical Institute

Document Type

Master's Dissertation

Degree Name

Master of Technology

Subject Name

Computer Science


Advance Computing and Microelectronics Unit (ACMU-Kolkata)


Bishnu, Arijit (ACMU-Kolkata; ISI)

Abstract (Summary of the Work)

The Bichromatic Biological Cell Sorting Problem1.1.1 MotivationRare cell population, e.g. adult stem cell, is available in very small quantities in samples that also have limited supply. Automatic cell sorting and isolation for recovery of such live cells is a challenging task. The method involves an enrichment step by magnetic or fluorescent cell sorting followed by manual or automatic cell picking or analysis [11]. Thus, applications in the medical, biological and pharmaceutical fields like stem cell research, cell therapy and cell based diagnostics need both microorganism detection and manipulation [26], [18], [14], [2], [19].A Lab-on-a-Chip (LOC) is a device that can integrate several laboratory functions on a single chip of very small size. LOCs can handle very small fluid volumes. LOCs with sensing, processing and actuation functions can serve this purpose [17]. Microorganisms can be manipulated or displaced from their location using dielectrophoresis (or DEP). DEP is a physical phenomenon in which a force is exerted on neutral particles when it is subject to nonuniform electric field. The microorganisms can also be detected using DEP cage approach [18] and impedance sensing [17]. Differences in permittivity and conductivity between the particles and the suspending medium is used for detecting and then manipulating the microorganisms. The manipulation is done by applying electric fields using DEP. Static DEP cages have been developed that can trap live individual cells into closed potential cages [11].To sum up the process of LOC, we have the power of detecting and manipulating or moving microorganisms. The microorganisms are manipulatedusing voltage differentials (electric fields) and moved so that they can be collected at desired locations. The samples are prepared on a cell array by culturing it with some reagent so that normal or desired samples can be differentiated from undesired ones. These are then manipulated using electric fields so that they are separated and trapped and collected at the corresponding DEP cages or receptors. By manipulation, we mean the microorganisms on the cell array are displaced towards their corresponding receptor. This way the cell array is exhausted of the microorganisms. Once the microorganisms are collected at their receptors, several biological tests may be performed on them. Thus, for an abstract model of the problem, we can assume the cell array to be represented by a matrix where each cell can be any of the three types: empty, desired and undesired. We have to empty the cell array by pushing the desired and undesired cells to their respective receptors. A similar problem is studied in [12].1.1.2 Problem DefinitionWe are given a matrix A of M ×N cells. Each such cell (i, j) (0 ≤ i ≤ M −1, 0 ≤ j ≤ N − 1), can have 3 possible values: Red (denoted as R), Blue (denoted as B) and Empty (denoted as E). Let Nr denote the number of R cells, Nb denote the number of B cells and Ne denote the number of E cells. So, Nr + Nb + Ne = M × N. We denote the cell in the i th row and j th column as (i, j). For a cell (i, j), we define its neighbourhood to be the set of cells N = {(i, j − 1),(i, j + 1),(i + 1, j),(i − 1, j)} if (i, j) does not lie on the horizontal or vertical boundaries of A. If (i, j) lies on the horizontal or vertical boundaries or the corners, then the neighborhood of (i, j) is an appropriate subset of N , e.g., the neighborhood of (0, N − 1) is {(0, N − 2),(1, N − 1)} and the neighborhood of (1, N − 1) is {(0, N − 1),(1, N − 2),(2, N − 1)}. A cell with value E can exchange its value with any of its neighbouring cells. A cell with value R or B can exchange its value only with a neighbouring E cell. In addition, a cell with value R (resp. B) can “merge” with a neighbouring cell if and only if that cell has value R (B resp.), with the value of the cell unchanged after the “merging” operation. Such exchanges are performed with the help of a voltage differential applied across such neighbouring cells. This can be done by using a manhattan wire layout beneath the cells. Such exchanges allow a cell to reach to its corresponding receptor. An R-receptor is located outside the matrix, adjacent to the cell (0, 0). Any R in this cell is removed by the R receptor, and hence can be replaced in cell (0, 0) by an E. Similarly, a B receptor is located outside the matrix, adjacent to the cell (N − 1, 0). Any B in this cell gets removed by the B-receptor, and is replaced in cell (N − 1, 0)by an E. So, the number of E cells increases in the matrix as the emptying process goes on. The R and B receptors provide a mechanism for emptying R and B cells from the matrix. Figure 1.1.2 shows an example.


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Creative Commons Attribution 4.0 International License
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