Set of tools to work with files created with Hamamatsu Orca cameras and their software (Hokawo and HCImage).

This class contains a few methods to load, view and handle HIS files generated with Hokawo (streaming) and Hammamatsu Orca cameras (teste on Orca Flash 2.8 and 4.0 and Hokawo versions 2.5 and 2.8).

One of the main advantages comapared with using Hokawo is that i can load and preview any frame on the file almost instantly. Without the need to read the whole file first.

Just copy his.m somewhere in your path

Create a new object with its constructor:

exp = his(); % This will open a uigetfile dialog to ask for the HIS file
exp = his('/path/to/his/file.his'); % To automatically load the file

The created object has a few public properties, namely numFrames, width, height, metadata, pixelType, bpp, fps, totalTime (self explanatory).

Now, if you want to pull a specific frame:

img = exp.getFrame(2); % Will pull frame number 2;

And to directly preview it (opens a figure and calls imagesc):

hFig = exp.previewFrame(2); % Returns the figure handle

Full working code to iterate through all the frames:

exp = his('/path/to/his/file.his'); % To automatically load the file
exp = exp.openStream();
for it = 1:exp.numFrames
  img = exp.getFrame(it);
  % Do something with the image
end
exp = exp.closeStream();

This HIS reader makes use of a precaching hack to predict frames positions, but if you have issues pulling specific frames, you might want to look at the precacheHISframes function inside the class.

Verification of precaching on incomplete HIS files

Based on the HISReader of The Open Microscopy Environment.

This script quickly opens as a VirtualStack the typical HIS files generated with Hokawo and Hamamatsu Orca cameras (tested on Orca Flash 2.8 and 4.0 and Hokawo versions 2.5 and 2.8). If you see 'Inconsistent METADATA' in the HIS parameters window it means that the stack might be corrupted (you will see that if the image starts to "travel"). This is due to a change in metadata length inside the HIS file and cannot be easily avoided without a sequential opening and/or precaching.

Based on the HISReader of The Open Microscopy Environment.

Copy the file HIS_opener.py somwhere inside the plugins folder in ImageJ. To download only that file press the Raw button and "Save As" in your browser.

Typical location is FIJI.app/plugins/Scripts/Plugins Restart ImageJ and HIS opener should appear at the bottom of the Plugins menu.

Select HIS opener from the ImageJ plugins menu and select the HIS file.

It looks like at some point Hokawo changed bit endianness. And I have no idea where that info is stored inside the HIS file (I am not even sure it is actually stored). So if the resulting movie makes no sense, you might have to change finfo.intelByteOrder to 1 in the script.

This script quickly opens as a VirtualStack the typical DCIMG files generated with HCImage and Hamamatsu Orca cameras (tested on Orca Flash 2.8 and 4.0 and HCImage Live 4.3).

Based on the Python module for reading Hamamatsu DCIMG files from Stuart Littlefair.

Copy the file DCIMG_opener.py somwhere inside the plugins folder in ImageJ. To download only that file press the Raw button and "Save As" in your browser.

Typical location is FIJI.app/plugins/Scripts/Plugins Restart ImageJ and DCIMG opener should appear at the bottom of the Plugins menu.

Select DCIMG opener from the ImageJ plugins menu and select the DCIMG file.