Cells&Maps 5.82

MS-Windows software that makes FACS and micrograph analysis easy.

Bitmap analysis with Cells&Maps
Cells&Maps is a program to analyse
immunocytochemistry images and FACS data for MS-Windows 2000 and up.

Carry out quantative analysis of fluorescence, cell shape, neurite length cell movements and cell number with Cells&Maps.
It takes (stacks of) bmp,tiff and jpg images and it outputs an illustrated vector drawing ready for publication.

(contextual) Help is provided in HTML.
Browse the online manual.


Cells&Maps is not a classical program for manipulating bitmaps such as Corel's Photopaint or Adobe's Photoshop. Where the latter programs take images as input, Cells&Maps takes a page that may contain multiple graphical elements amongst which bitmaps. The other graphical elements may originate from other programs of the Serf Software Suite, such as graphs created by Electrophy or heatmaps created by Clusters.
Hence, Bitmaps are imported and manipulated on the drawing sheet, allowing to carry out semi-automatic optical density measurements on images of cells, gels and blots:                                              or to align multiple micrographs to measure neurite length:

gel quantification with Cells&Maps              

Basic bitmap manipulations include: noise removal, filtering, separate RGB components or inversely merge three (gray scale) images into a RGB image, convert gray scale into pseudo colours, carry out mathematical operations between maps (e.g. ORing, ANDing, subtracting or adding images), change image contrast, thresholding and image convolution. Improve the sharpness of blurry images using inverse Wiener filtering:
wiener filter

The macro option lets you record your actions to be run later if the same sequence of manipulations has to be carried out on multiple images.

Stacks of bitmaps may be animated or analysed with a single instruction. In the example shown below, the sequence of images taken on the square was transformed into the differentiated sequence. Image differentiation allows detection and quantification of movements such as cell contraction and migration.
Cell movement detection with Czlls&Maps                    

Fluorescence Activated Cell Sorting (FACS) data in *.fcs or *.lmd formats can be read and analysed graphically. Draw a closed figure over the data delineating a subset and continue analysis with this subset.Scripts that you create help to carry out repetitive jobs briskly.

Statistical tests of the results are carried out in spreadsheet columns: linear correlation, chi-2 test, Student's t-test, Fisher's F-test, Tukey's q-test (one-way anova).
Cells&Maps is amply documented and help is provided in several ways: by key word search, by context and by menu item. The doc file includes a comprehensive step by step tutorial. Under Windows 10, the tutorial can be found by clicking "All applications" in the start menu. Then look for the Cells&Maps folder, which contains Cells&Maps.doc.