Python and ImageJ  implementations of spatial speckle contrast calculations and associated simulated and experimental datasets
Creators: name: Pain, Frédéric
name: Chammas, Marc
Publisher: name: Zenodo
Year: 2025
Subjects: subject: Diagnostic imaging
subject: Optics
subject: Fluid dynamics
subject: Laser Speckle Imaging
subject: Data Analysis
subject: Optics and Photonics/methods
subject: Optics and Photonics/statistics &amp; numerical data
subject: Blood Flow Velocity

description: Datasets files

These are the three datasets of raw time integrated speckle images  used in a submitted publication.

These are mutlitif files that can be open for rapid examination in FIJI (ImageJ).

Dataset 1 is composed of simulated time-integrated speckle patterns images

2 files :   dataset1_tc1ms.tif and dataset1_tc01ms.tif

Images are 32-bit and 1000 x 1000 pixels. For both datasets in dataset 1, the following simulation parameters are used :3 pixels per speckle ; rho = 1 ie (100% moving scatterers and no static scatterers);a decorrelation function g1(tc,n,rho) with n = 1 parameter corresponding to ordered flow and mutliple scattering as described in James E. et al . Simulation of statistically accurate time-integrated dynamic speckle patterns in biomedical optics Opt Lett 46 4390-4393 (2021). 

Each data set is composed of 15 images corresponding to simulated exposure times of  0.05, 0.1, 0.2, 0.5, 0.8, 1, 2, 3.5, 5, 10, 15, 20, 30, 40 and 60 ms



For Dataset1_tc1ms.tif, the decorrelation time was set to 1 ms.

For Dataset1_tc01ms.tif, the decorrealtion time was set to 0.1 ms.


Dataset 2  is composed of experimental raw time-integrated speckle images acquired in vivo at the surface of an anesthetized mouse

1 file dataset_2_invivo_MESI_data.tif

Images are 16-bit ( camera bit depth = 12-bit) and  1372 * 1046 pixels. They are time-integrated raw speckle data acquired sucessively using a modulated laser pulse method with the set-up and methods described in  Soleimanzad, H. et al. Multiple speckle exposure imaging for the study of blood flow changes induced by functional activation of barrel cortex and olfactory bulb in mice. Neurophotonics 6, 015008 (2019).

The data set is composed of 774 images cycling through exposure times of  1, 2, 5, 10, 15 and 20 ms. This correspond to 129 MESI sequences of 6 exposure times.

In vivo imaging was carried out in accordance with the European Directive 2010/63/UE (Ethical project \#CEB-03-2018) regarding the care and use of laboratory animals. In vivo recordings were carried out in 4-months old, anesthetized mice (male, C57BL6, mean weight = 48 g) after a craniotomy was performed over the barrel cortex. Anesthesia was carried out with a cocktail of ketamine (100 mg/kg Imalgen) and metedomidine (0.5 mg/kg), injected intraperitoneally. The anesthesia level was adjusted as necessary throughout the experiment. Surgery begins when the mouse no longer responds to hindpaw pinch. During the entire experiment, the animal was placed on a thermostatically controlled heating pad. Body temperature was maintained rectally at 37°C. After the animal was secured in a stereotactic frame, imaging was carried out over regions of about 3 x 2 mm2 over the barrel cortex. A low-temperature agarose layer (1.2\%) and a microscope coverslip were placed over dura-matter.

 

Scripts files

Both files are fully commented

Python implementations of speckle spatial contrast calculations methods 

1 file Ks_methods.py

ImageJ macro  for speckle spatial contrast calculation for a 3D stack of  2D  images in .tif format.

1 file KsIJ.ijm