# Timelapse of timelapses and z-stacks¶

This notebook shows how to repeatedly acquire a short time series and then a z stack at a set with a set delay in between.

In this example we acquire a time series of `duration = 2`

seconds and then a z stack parameterized by `z_start = -2.5; z_end = 2.5; z_step = 0.25`

every `subset_interval = 20`

seconds for `total_duration = 60`

seconds. That is, we acquire data subsets containing a 2 second time series and a 5 micrometer z stack every 20 seconds over the span of 60 seconds.

Using `pycro-manager`

this set of acquisition events is encoded as follows:

```
events = []
for s in range(num_subsets):
for t in range(num_time_points):
events.append(
{
"axes": {"subset": s, "time": t, "z": 0},
"z": z_sequence[0],
"min_start_time": s * subset_interval,
}
)
for z in range(num_z_slices):
events.append(
{
"axes": {"subset": s, "time": num_time_points, "z": z},
"z": z_sequence[z],
"min_start_time": s * subset_interval,
}
)
```

```
[ ]:
```

```
import numpy as np
from pycromanager import Acquisition, Bridge, multi_d_acquisition_events
```

## Construct java objects¶

```
[8]:
```

```
bridge = Bridge()
mmc = bridge.get_core()
mmStudio = bridge.get_studio()
```

## Set acquisition parameters¶

```
[9]:
```

```
# Data set parameters
path = r"C:\test"
name = "pycromanager test"
total_duration = 60 # in seconds
subset_interval = 20 # in seconds
# z stack parameters
z_start = -2.5
z_end = 2.5
z_step = 0.25
relative = True
sequence = False
# time series parameters
duration = 2 # in seconds
framerate = 10
num_subsets = np.ceil(total_duration / subset_interval).astype(np.int)
num_time_points = duration * framerate
z_sequence = np.arange(z_start, z_end + z_step, z_step)
num_z_slices = len(z_sequence)
```

## Prepare for acquisition¶

```
[10]:
```

```
# setup cameras -- this property may change depending on the particular camera used
mmc.set_property("Camera", "Framerate", framerate)
# setup z stage
z_stage = mmc.get_focus_device()
if relative:
z_pos = mmc.get_position(z_stage)
z_sequence += z_pos
if sequence:
mmc.set_property(z_stage, "UseSequence", "Yes")
bridge.close()
```

## Generate events¶

```
[11]:
```

```
events = []
for s in range(num_subsets):
for t in range(num_time_points):
events.append(
{
"axes": {"subset": s, "time": t, "z": 0},
"z": z_sequence[0],
"min_start_time": s * subset_interval,
}
)
for z in range(num_z_slices):
events.append(
{
"axes": {"subset": s, "time": num_time_points, "z": z},
"z": z_sequence[z],
"min_start_time": s * subset_interval,
}
)
```

## Acquire data¶

```
[12]:
```

```
with Acquisition(directory=path, name=name) as acq:
acq.acquire(events)
```