joda01 / evanalyzer

EVAnalyzer 1 - EV analyzing plugin for Fiji

• 👋 Hi, I’m @joda01

evanalyzer's Issues

Add open Result in Excel button

Add area size and saturation of EV

Place preview picture beside main window when opening preview picture

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Analyses sometimes slow

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Add Update function

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Cannot handle special chars in filenames

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Margin crop and z projection settings are not stored in excel report

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Support smaller screens

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It is not possible to select CY7

Man kann den Cy7-Channel nicht auswählen, wenn ich den Cy7-Kanal auswähle bekomme ich eine Fehlermeldung.

Make Z Projection configurable

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Control pictures not created correct

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Control pictures not created

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Control pictures

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java.lang.ArrayIndexOutOfBoundsException: 7
at org.danmayr.imagej.algorithm.pipelines.Pipeline.saveControlImages(Pipeline.java:185)
at org.danmayr.imagej.algorithm.pipelines.ExosomColoc.startPipeline(ExosomColoc.java:79)
at org.danmayr.imagej.algorithm.pipelines.Pipeline.ProcessImage(Pipeline.java:101)
at org.danmayr.imagej.algorithm.FileProcessor.walkThroughFiles(FileProcessor.java:167)
at org.danmayr.imagej.algorithm.FileProcessor.run(FileProcessor.java:99)

Create control pictures with ROI

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Apply Gauss does not work in preview

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Implement algorithm to count EVs per cell

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Support 9 channels

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Add possibility to apply additionally preprocessing filters.

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Add some more channel selection possibilities

Add:
CY3 (red)
CY5 (red)
CY7 (red)
GFP (green)
DAPI (blau)

Bug in in cell counting on windows

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New coloc method

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Support detection of fluorescent cells

Remember last open path

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Preview not working

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Wrong coloc in CH3

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Multi coloc picture calculation

Und eine weitere Erleichterung für uns wäre wenn man die Colocalization von mehreren Bildern auf einmal berechnen könnte. Zum Beispiel wenn ich ein Bild mit 4 Kanälen habe, den ersten als Background verwendet, den C=1 mit C=2 vergleicht, C=2 mit C=3 und C=1 mit C=3.

Support CZI image format

• TIF
• JPEG
• NEF (Nicon)
• CZI (Zeiss)

Calculate size in real values instead of pixels

Implement field to define the pixel to size ratio

Problem generating multi folder excel report

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Report name ot correct under Windows

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Gray scale value is wrong

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Add possibility to just count EVs with one channel images

If Channel 0 is set to Off and Channel 1 to ON also Channel 0 is taken for analyzing

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Make report builder faster

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Make it possible to set particle size filter for each channel

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Improve report generation

Wenn man Cy5 als C=0 einstellt und Cy3 als C=1 diese Ergebnisse, dann im Results sheet umgekehrt angezeigt werden, also Cy5 als C=1 und Cy3 als C=0. Das hat am Anfang ein wenig zu Verwirrungen geführt.

Calculate coloc of three channels

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Open first available picture when opening preview

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Show programm version in Settings tab

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Improve speed of in cell EV counting

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Create overlay image for in cell counting

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Tetra specs are not subtracted correct

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Improve TetraSpeck detection

Original message from @maria:

Ich habe beobachtet, dass in manchen Fotos immer noch einige TetraSpeck beats übersehen werden. Diese TetraSpeck beats sind allerdings gleich hell wie die die er detektiert hat. Weiters habe ich gesehen, dass mache Spots als TetraSpeck beat erkannt werden, die aber kein Signal im FITC-Kanal zeigen. Ich habe dir ein Beispiel angehängt (Originales TetraSpeck image und Kontrollbild), da kann man vorallem an der rechten Seite sehen, dass er in manchen Bereichen ein nicht vorhandenes TetraSpeck beat erkannt hat.

Add settings summary to report sheet

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Implement in Cell Counter

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Preview is only applied on one channel

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Add including directory to results file

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Improve preview speed

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Add feature to remove cells at edges

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Find interrelated EVs in Coloc Algo and display the Intensity of them

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Add croping feature

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Coloc Count with just one channel does not work

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