From dff787f91dd260474c04655abdd3d15201469efd Mon Sep 17 00:00:00 2001 From: Joott Date: Tue, 21 May 2019 02:25:51 +0200 Subject: [PATCH] Update generated documentation for version 0.0.1 --- DilutionExperiment.html | 6 +++--- FunctionExplanation.html | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/DilutionExperiment.html b/DilutionExperiment.html index a2beda9..9ca3183 100644 --- a/DilutionExperiment.html +++ b/DilutionExperiment.html @@ -38,13 +38,13 @@

Counting

To determine the effectiveness of the Cell Counter, I compared it to two different other counting methods. One of them was manual counting using the Neubauer counting chamber, the other was counting the cells with a Coulter Counter. For that i took a cell suspension with ~1.35 * 10^7 cells and set up a serial dilution by always halving the amount up to 1:16. -I took 3 measurements for each timepoint. One measurement for both, the Cell Counter and the manual counting consists of three seperate images.

+I took 3 measurements for each timepoint. One measurement for both, the Cell Counter and the manual counting, consists of three seperate images.

Here you can see the result of those measurements:

-
+


diff --git a/FunctionExplanation.html b/FunctionExplanation.html index 4101e58..e322f1b 100644 --- a/FunctionExplanation.html +++ b/FunctionExplanation.html @@ -69,7 +69,7 @@

Process

filePath is the path of the image. Height and width can be filled with the same result from the Filter.squareCalculator. Radius gets the result from Filter.cellRadiusCalculator. thresholdMultiplier is a multiplier for the cutoff after the wavelet transformation. It has to be higher the closer in intensity the background to the cells is. The threshold function in the -pipeline contains a boolean for determining whether the cells have a positive or negative value. In all cases so far the intensities were negative. if for some reason they are positive, +pipeline contains a boolean for determining whether the cells have a positive or negative value. In all cases so far the intensities were negative. If for some reason they are positive, the boolean has to be changed to "true". The chart which is returned in the resulting tuple serves visualization purposes. this functionality can be removed without consequences.

@@ -79,7 +79,7 @@

Process 

1:

This function is a convenience function which applies the previous function to a whole folder with images. It takes a folderpath instead of the filepath and processes all images in that folder.

-

Alternative uses

+

Possible Variants

The threshold function currently used in the Pipeline.processImage is based on the maximum intensities in the pictures. An alternative threshold function exists which is based on a percentile cutoff. It can be used in place of the other function, although its performance is worse with changing cell numbers.

To count cells in petri dishes, the Filter.rectangleSelectorCenter function in the pipeline has to be replaced with: