allensdk.brain_observatory.roi_masks module¶
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class
allensdk.brain_observatory.roi_masks.Mask(image_w, image_h, label, mask_group)[source]¶ Bases:
objectAbstract class to represent image segmentation mask. Its two main subclasses are RoiMask and NeuropilMask. The former represents the mask of a region of interest (ROI), such as a cell observed in 2-photon imaging. The latter represents the neuropil around that cell, and is useful when subtracting the neuropil signal from the measured ROI signal.
This class should not be instantiated directly.
Parameters: - image_w: integer
Width of image that ROI resides in
- image_h: integer
Height of image that ROI resides in
- label: text
User-defined text label to identify mask
- mask_group: integer
User-defined number to help put masks into different categories
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class
allensdk.brain_observatory.roi_masks.NeuropilMask(w, h, label, mask_group)[source]¶ Bases:
allensdk.brain_observatory.roi_masks.Mask-
init_by_mask(border, array)[source]¶ Initialize mask using spatial mask
Parameters: - border: float[4]
Coordinates defining useable area of image. See create_roi_mask().
- array: integer[image height][image width]
Image-sized array that describes the mask. Active parts of the mask should have values >0. Background pixels must be zero
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class
allensdk.brain_observatory.roi_masks.RoiMask(image_w, image_h, label, mask_group)[source]¶ Bases:
allensdk.brain_observatory.roi_masks.Mask-
init_by_mask(border, array)[source]¶ Initialize mask using spatial mask
Parameters: - border: float[4]
Coordinates defining useable area of image. See create_roi_mask().
- roi_mask: integer[image height][image width]
Image-sized array that describes the mask. Active parts of the mask should have values >0. Background pixels must be zero
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allensdk.brain_observatory.roi_masks.calculate_roi_and_neuropil_traces(movie_h5, roi_mask_list, motion_border)[source]¶ get roi and neuropil masks
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allensdk.brain_observatory.roi_masks.calculate_traces(stack, mask_list, block_size=100)[source]¶ Calculates the average response of the specified masks in the image stack
Parameters: - stack: float[image height][image width]
Image stack that masks are applied to
- mask_list: list<Mask>
List of masks
Returns: - float[number masks][number frames]
This is the average response for each Mask in each image frame
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allensdk.brain_observatory.roi_masks.create_neuropil_mask(roi, border, combined_binary_mask, label=None)[source]¶ Conveninece function to create and initializes a Neuropil mask. Neuropil masks are defined as the region around an ROI, up to 13 pixels out, that does not include other ROIs
Parameters: - roi: RoiMask object
The ROI that the neuropil masks will be based on
- border: float[4]
Coordinates defining useable area of image. See create_roi_mask().
- combined_binary_mask
List of pixel coordinates (x,y) that define the mask
- combined_binary_mask: integer[image_h][image_w]
Image-sized array that shows the position of all ROIs in the image. ROI masks should have a value of one. Background pixels must be zero. In other words, ithe combined_binary_mask is a bitmap union of all ROI masks
- label: text
User-defined text label to identify the mask
Returns: - NeuropilMask object
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allensdk.brain_observatory.roi_masks.create_roi_mask(image_w, image_h, border, pix_list=None, roi_mask=None, label=None, mask_group=-1)[source]¶ Conveninece function to create and initializes an RoiMask
Parameters: - image_w: integer
Width of image that ROI resides in
- image_h: integer
Height of image that ROI resides in
- border: float[4]
Coordinates defining useable area of image. If the entire image is usable, and masks are valid anywhere in the image, this should be [(image_w-1), 0, (image_h-1), 0]. The following constants help describe the array order:
RIGHT_SHIFT = 0
LEFT_SHIFT = 1
DOWN_SHIFT = 2
UP_SHIFT = 3
When parts of the image are unusable, for example due motion correction shifting of different image frames, the border array should store the usable image area
- pix_list: integer[][2]
List of pixel coordinates (x,y) that define the mask
- roi_mask: integer[image_h][image_w]
Image-sized array that describes the mask. Active parts of the mask should have values >0. Background pixels must be zero
- label: text
User-defined text label to identify mask
- mask_group: integer
User-defined number to help put masks into different categories
Returns: - RoiMask object